<PAGE>

      As filed with the Securities and Exchange Commission on July 23, 2001

                                                   REGISTRATION NO. 333-

===============================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                              ---------------------

                                    FORM S-8
                             REGISTRATION STATEMENT
                                    UNDER THE
                             SECURITIES ACT OF 1933

                              ---------------------

                       VERTEX PHARMACEUTICALS INCORPORATED
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)


       MASSACHUSETTS                                            04-3039129
(STATE OR OTHER JURISDICTION                                 (I.R.S. EMPLOYER
OF INCORPORATION OR ORGANIZATION)                           IDENTIFICATION NO.)


                               130 WAVERLY STREET
                            CAMBRIDGE, MA 02139-4242
                    (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)


                 AURORA BIOSCIENCES CORPORATION 1996 STOCK PLAN

           AURORA BIOSCIENCES CORPORATION EMPLOYEE STOCK PURCHASE PLAN

                  1993 STOCK OPTION PLAN OF PANVERA CORPORATION

  NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND UTE MUH

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                              DOUGLAS JOHN BARTELS

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                             STEVE C. WINANS, PH.D.

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                             MICHAEL J. WELSH, M.D.

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                              PAUL V. DUNLAP, PH.D.

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                              J. WOODLAND HASTINGS

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                                 UTE MUH, PH.D.

            STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                            JAMES A. ROMESSER, PH.D.
                           (FULL TITLES OF THE PLANS)


                JOSHUA BOGER, PRESIDENT & CHIEF EXECUTIVE OFFICER
                       VERTEX PHARMACEUTICALS INCORPORATED
                               130 WAVERLY STREET
                            CAMBRIDGE, MA 02139-4242

                                 (617) 577-6000
    (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA
                           CODE, OF AGENT FOR SERVICE)

                              ---------------------

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>

============================================================================================================================
                                                              Proposed               Proposed
                                                               maximum                maximum
           Title of                   Amount to be         offering price            aggregate               Amount of
 securities to be registered         registered(1)          per share(2)          offering price(2)     registration fee(3)
----------------------------------------------------------------------------------------------------------------------------
<S>                                <C>                  <C>                    <C>                     <C>


 Common Stock, $.01 par value       2,757,632 shares           $14.10                $38,882,611              $ 9,721
                                      310,062 shares           $39.28                $12,179,236              $ 3,045
                                    ---------                                                                 -------
                                    3,067,694 shares                                                          $12,766
                                                                                                              $(2,912)
                                                                                                              $ 9,854
----------------------------------------------------------------------------------------------------------------------------
 Rights to Purchase Series A             (4)                    (4)                    (4)                     None
     Junior Participating
       Preferred Stock
============================================================================================================================
</TABLE>

(1)      The number of shares of Common Stock, par value $.01 per share ("Common
         Stock"), stated above consists of the aggregate number of shares which
         may be sold (i) upon exercise of options which have been granted under
         the Aurora Biosciences Corporation 1996 Stock Plan, 1993 Stock Option
         Plan of PanVera Corporation and Option Agreements between Quorum
         Sciences, Inc. and certain of its employees and shares of stock which
         may hereafter be sold under the Aurora Biosciences Corporation Employee
         Stock Purchase Plan (collectively, the "Plans"). The maximum number of
         shares which may be sold upon exercise of options granted under the
         Plans are subject to adjustment in accordance with certain
         anti-dilution and other provisions of the Plans. Accordingly, pursuant
         to Rule 416 under the Securities Act of 1933, as amended (the
         "Securities Act"), this Registration Statement covers, in addition to
         the number of shares stated above, an indeterminate number of shares
         which may be subject to grant or otherwise issuable after the operation
         of any such anti-dilution and other provisions.

(2)      Estimated solely for the purpose of determining the registration fee in
         accordance with Rule 457(c) and (h) under the Securities Act of 1933,
         as amended, as follows: (i) in the case of shares of Common Stock which
         may be purchased on the exercise of outstanding options, the fee is
         calculated based on the weighted average exercise price of the
         outstanding options; and (ii) in the case of shares of Common Stock
         which may be purchased under the Aurora Biosciences Corporation
         Employee Stock Purchase Plan, the price of which is unknown, the fee is
         calculated on the basis of the average high and low sales prices per
         share of the Common Stock on The Nasdaq National Market of $39.28 on
         July 18, 2001 within 5 business days prior to filing this registration
         statement.

(3)      Pursuant to Rule 457, the Registrant prepaid the registration fee for
         586,977 shares under the Plans when it registered up to 14,725,000
         shares of Common Stock pursuant to Registration Statement on Form S-4
         (File Number 333-61480) initially filed on May 23, 2001. Therefore,
         $2,912 is offset against the total currently due filing fee of
         $12,766.

(4)      No separate consideration will be received for the Rights.

===============================================================================


<PAGE>


                                EXPLANATORY NOTE

         Vertex Pharmaceuticals Incorporated (the "Registrant") hereby files
this Registration Statement on Form S-8 relating to its Common Stock, par value
$0.01 per share, which may be sold upon the exercise of options granted: (i)
under the Aurora Biosciences Corporation ("Aurora") 1996 Stock Plan, (ii) under
the Aurora Employee Stock Purchase Plan, (iii) under the 1993 Stock Option Plan
of PanVera Corporation and (iv) under the Stock Option Agreements between Quorum
Sciences, Inc. and certain of its employees (collectively the "Plans").

         Pursuant to the merger (the "Merger") provided for in the Agreement
and Plan of Merger, dated as of April 29, 2001, among the Registrant, Aurora
and Ahab Acquisition Sub, Inc. ("Ahab Sub"), a wholly owned subsidiary of the
Registrant, Ahab Sub was merged into Aurora and Aurora became a wholly owned
subsidiary of the Registrant effective July 18, 2001. Upon consummation of
the Merger, the Registrant assumed the obligations of Aurora under the Plans
and each option is governed by the same terms and conditions that governed
the applicable option immediately prior to the Merger except that:

         o        each such option is exercisable for the number of shares
                  of the Registrant's common stock equal to the number of shares
                  of Aurora common stock issuable upon exercise of the option
                  multiplied by 0.62, rounded down to the nearest whole share;

         o        the per share exercise price for the shares of the
                  Registrant's common stock issuable upon the exercise of the
                  assumed option is equal to the exercise price per share
                  of the Aurora option divided by 0.62, rounded up to the
                  nearest whole cent; and

         o        each outstanding restricted share of Aurora common stock was
                  converted into the number of restricted shares of the
                  Registrant's Common Stock that is equal to the product of 0.62
                  multiplied by the shares of Aurora common stock subject to the
                  award.

         This Registration Statement relates to the Common Stock of the
Registrant issuable upon exercise of the options or which may be sold pursuant
to the Plans as follows:

         o        2,616,985 shares subject to the Aurora 1996 Stock Plan.

         o        310,062 shares subject to the Aurora Employee Stock Purchase
                  Plan.

         o        137,947 shares subject to the 1993 Stock Option Plan of
                  PanVera Corporation.

         o        2,700 shares subject to the Stock Option Agreements between
                  Quorum Sciences, Inc. and certain of its employees.


<PAGE>


                                     PART I

         In accordance with the instructional Note to Part I of Form S-8 as
promulgated by the Securities and Exchange Commission, the information specified
by Part I of Form S-8 has been omitted from this Registration Statement on Form
S-8 for offers of Common Stock pursuant to the Aurora 1996 Stock Plan, the
Aurora Employee Stock Purchase Plan, the 1993 Stock Option Plan of PanVera
Corporation, and the Stock Option Agreements between Quorum Sciences, Inc. and
certain of its employees.



                                      I-1

<PAGE>


                                    PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT


ITEM 3.  INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE.

         The following documents filed by the Registrant or Aurora Biosciences
Corporation with the Commission are incorporated herein by reference:

         (a) The Registrant's Annual Report on Form 10-K for the fiscal year
ended December 31, 2000 (filing date March 26, 2001).

         (b) The Registrant's Quarterly Report on Form 10-Q (Commission File No.
000-19319) for the quarter ended March 31, 2001 (filing date May 15, 2001).

         (c) The Registrant's Current Report on Form 8-K for the April 29, 2001
event (filing date April 30, 2001).

         (d) Aurora's Annual Report on Form 10-K for the fiscal year ended
December 31, 2000 (filing date March 15, 2001).

         (e) Aurora's Quarterly Report on Form 10-Q for the quarterly period
ended March 31, 2001 (filing date May 11, 2001).

         (f) Aurora's Current Report on Form 8-K for the February 7, 2001 event
(filing date February 7, 2001).

         (g) Aurora's Current Report on Form 8-K for the March 1, 2001 event
(filing date March 7, 2001).

         (h) Aurora's Current Report on Form 8-K for the April 2, 2001 event
(filing date April 5, 2001).

         (i) Aurora's Current Report on Form 8-K for the April 29, 2001 event
(filing date April 30, 2001).

         (j) Aurora's Current Report on Form 8-K for the March 1, 2001 event
(filing date May 18, 2001), which contains financial statements and related
information that restate and supercede the financial statements and related
information in Aurora's Annual Report on Form 10-K for the fiscal year ended
December 31, 2000, filed on March 15, 2001.

         (k) Description of the Registrant's Common Stock included in the
Registrant's Registration Statement on Form S-4 (Reg. No. 333-61480) filed under
the Securities Act of 1933, including any amendment or report filed for the
purpose of updating such description.

         All reports and other documents filed by the Registrant after the date
hereof pursuant to Sections 13(a), 13(c), 14 and 15(d) of the Securities
Exchange Act of 1934 prior to the filing of a post-effective amendment which
indicates that all securities offered hereby have been sold or which deregisters

                                      II-1

<PAGE>

all securities then remaining unsold, shall be deemed to be incorporated by
reference herein and to be part hereof from the date of filing of such reports
and documents.

ITEM 4.  DESCRIPTION OF SECURITIES.

         Not applicable.

ITEM 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL.

         Not applicable.

ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

         Part D of Article 6 of the Restated Articles of Organization of the
Registrant provides that no director of the Registrant shall be personally
liable to the Registrant or its stockholders for monetary damages for breach of
fiduciary duty as a director. Such paragraph provides further, however, that, to
the extent provided by applicable law, it will not eliminate or limit the
liability of a director (i) for any breach of the director's duty of loyalty to
the Registrant or its stockholders, (ii) for acts or omissions not in good faith
or which involve intentional misconduct or a knowing violation of law, (iii) for
distributions made in violation of the Registrant's Restated Articles of
Organization or which are made when the Registrant is insolvent or which renders
it insolvent, (iv) for loans made to officers or directors of the Registrant
which are not repaid if the director has voted for such loans and they have not
been approved or ratified as loans reasonably expected to benefit the
Registrant, by a majority of directors who are not recipients of such loans or
the holders of a majority of voting shares, which holders are not recipients of
such loans, and (v) for any transactions from which the director derived an
improper personal benefit.

         Article V of the Registrant's By-laws provides that the Registrant
shall indemnify each of its directors and officers (including persons who serve
at the Registrant's request as a director, officer or trustee of another
organization in which the Registrant has any interest, direct or indirect, as a
stockholder, creditor or otherwise or who serve at the Registrant's request in
any capacity with respect to any employee benefit plan) against all liabilities
and expenses, including amounts paid in satisfaction of judgments, in compromise
or as fines and penalties and counsel fees reasonably incurred by such director
or officer in connection with the defense or disposition of any action, suit or
other proceeding, whether civil or criminal, in which such director or officer
may be involved or with which such person may be threatened, while in office or
thereafter, by reason of such person's being or having been such a director,
officer or trustee, except with respect to any matter as to which such director
or officer shall have been adjudicated in any proceeding not to have acted in
good faith in the reasonable belief that such director's or officer's action was
in the best interest of the Registrant or, to the extent that such matter
relates to service with respect to an employee benefit plan, in the best
interest of the participants or beneficiaries of such employee benefit plan.

         As to any matter disposed of by a compromise payment by any such
person, pursuant to a consent decree or otherwise, Article V of the Registrant's
By-laws provides that no indemnification shall be provided to such person for
such payment or for any other expenses unless such compromise has been approved
as in the best interest of the Registrant, after notice that it involves such
indemnification (i) by a disinterested majority of the directors then in office,
(ii) by a majority of the disinterested directors then in office, provided there
has been obtained an opinion in writing of independent legal counsel to the
effect

                                      II-2

<PAGE>

that such director or officer appears to have acted in good faith in the
reasonable belief that such person's action was in the best interest of the
Registrant, or (iii) by the holders of a majority of the outstanding stock at
the time entitled to vote for directors, voting as a single class, exclusive of
any stock owned by any interested director or officer.

         Article V of the Registrant's By-laws provides that expenses, including
counsel fees, reasonably incurred by any director or officer in connection with
the defense or disposition of any such action, suit or other proceeding may be
paid from time to time by the Registrant at the discretion of a majority of the
disinterested directors then in office, in advance of the final disposition
thereof, upon receipt of an undertaking by such director or officer to repay the
Registrant the amounts so paid if it is ultimately determined that
indemnification for such expenses is not authorized under Article V of the
By-laws, which undertaking may be accepted by the Registrant without reference
to the financial ability of such director or officer to make repayment.

         Article V of the Registrant's By-laws gives the Board of Directors of
the Registrant the power to authorize the purchase and maintenance of insurance,
in such amounts as the Board of Directors may from time to time deem
appropriate, on behalf of any person who is or was a director, officer or agent
of the Registrant, or who is or was serving at the request of the Registrant as
a director, officer or agent of another organization in which the Registrant has
any interest, direct or indirect, as a shareholder, creditor or otherwise, or
with respect to any employee benefit plan, against any liability incurred by
such person in any such capacity, or arising out of such person's status as such
agent, whether or not such person is entitled to indemnification by the
Registrant pursuant to Article V or otherwise and whether or not the Registrant
would have the power to indemnify the person against such liability.

         Section 13(b)(1 1/2) of the Massachusetts Business Corporation Law,
Chapter 156B of the General Laws of Massachusetts (the "MBCL") authorizes the
provisions, described above, contained in Part D of Article 6 of the Restated
Articles of Organization of the Registrant.

         Section 67 of the MBCL authorizes the provisions, described above,
contained in Article V of the By-laws of the Registrant.

         Section 65 of the MBCL provides that performance by a director, officer
or incorporator of such person's duties in good faith and in a manner such
person reasonably believes to be in the best interest of the corporation, and
with such care as an ordinary prudent person in a like position would use under
similar circumstances, shall be a complete defense to any claim asserted against
such director, officer or incorporator, except as otherwise expressly provided
by statute, by reason of such person's being or having been a director, officer
or incorporator of the corporation.


ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED.

         Not applicable.

ITEM 8.  EXHIBITS.

         4.1      Specimen Common Stock Certificate (Filed as Exhibit 4.1 to the
                  Registrant's Registration Statement on Form S-1 (Registration
                  No. 33-40966) or amendments thereto and incorporated herein by
                  reference).

                                      II-3

<PAGE>

         4.2      Restated Articles of Organization filed with the Commonwealth
                  of Massachusetts on July 31, 1991 (Filed as Exhibit 3.1 to the
                  Registrant's Registration Statement on Form S-4 (Reg. No.
                  333-61480) filed on May 23, 2001, and incorporated herein by
                  reference).

         4.3      By-Laws, as amended and restated as of March 12, 2001 (Filed
                  as Exhibit 3.5 to the Registrant's Registration Statement on
                  Form S-4 (Reg. No. 333-61480) filed on May 23, 2001, and
                  incorporated herein by reference).

         5        Opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
                  as to the legality of shares being registered.

         23.1     Consent of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
                  (included in opinion of counsel filed as Exhibit 5).

         23.2     Consent of PricewaterhouseCoopers LLP, Independent
                  Accountants.

         23.3     Consent of Ernst & Young LLP, Independent Auditors.

         23.4     Consent of Arthur Andersen LLP.

         23.5     Consent of KPMG LLP.

         24       Power of Attorney to file future amendments (set forth on the
                  signature page of this Registration Statement.)

         99.1     Aurora Biosciences Corporation 1996 Stock Plan, as amended.

         99.2     Aurora Biosciences Corporation Employee Stock Purchase Plan,
                  as amended, and related offering document.

         99.3     1993 Stock Option Plan of PanVera Corporation.

         99.4     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Ute Muh.

         99.5     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Douglas John Bartels.

         99.6     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Steve C. Winans, Ph.D.

         99.7     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Michael J. Welsh, M.D.

         99.8     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Paul V. Dunlap, Ph.D.

         99.9     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and J. Woodland Hastings, Ph.D.

         99.10    Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Ute Muh, Ph.D.

         99.11    Stock Option Agreement between Quorum Sciences, Inc. and James
                  A. Romesser, Ph.D.

                                      II-4

<PAGE>

ITEM 9.  UNDERTAKINGS.

(a)      The undersigned Registrant hereby undertakes:

         (1) To file, during any period in which offers or sales are being made,
         a post-effective amendment to this Registration Statement:

                  (i) To include any prospectus required by Section 10(a)(3) of
                  the Securities Act of 1933;

                  (ii) To reflect in the prospectus any facts or events arising
                  after the effective date of the Registration Statement (or the
                  most recent post-effective amendment thereof) which,
                  individually or in the aggregate, represents a fundamental
                  change in the information set forth in the Registration
                  Statement. Notwithstanding the foregoing, any increase or
                  decrease in volume of securities offered (if the total dollar
                  value of securities offered would not exceed that which was
                  registered) and any deviation from the low or high end of the
                  estimated maximum offering range may be reflected in the form
                  of prospectus filed with the Commission pursuant to Rule
                  424(b) if, in the aggregate, the changes in volume and price
                  represent no more than a 20% change in the maximum aggregate
                  offering price set forth in the "Calculation of Registration
                  Fee" table in the effective Registration Statement.

                  (iii) To include any material information with respect to the
                  plan of distribution not previously disclosed in the
                  Registration Statement or any material change to such
                  information in the Registration Statement;

                           PROVIDED, HOWEVER, that paragraphs (a)(1)(i) and
                  (a)(1)(ii) do not apply if the Registration Statement is on
                  Form S-3, Form S-8 or Form F-3, and the information required
                  to be included in a post-effective amendment by those
                  paragraphs is contained in periodic reports filed with or
                  furnished to the Commission by the Registrant pursuant to
                  Section 13 or Section 15(d) of the Securities Exchange Act of
                  1934 that are incorporated by reference in this Registration
                  Statement.

         (2) That, for the purpose of determining any liability under the
         Securities Act of 1933, each such post-effective amendment shall be
         deemed to be a new registration statement relating to the securities
         offered therein, and the offering of such securities at that time shall
         be deemed to be the initial bona fide offering thereof.

         (3) To remove from registration by means of a post-effective amendment
         any of the securities being registered which remain unsold at the
         termination of the offering.

(b)      The undersigned Registrant hereby undertakes that, for purposes of
         determining any liability under the Securities Act of 1933, each filing
         of the Registrant's annual report pursuant to Section 13(a) or Section
         15(d) of the Securities Exchange Act of 1934 that is incorporated by
         reference in this Registration Statement shall be deemed to be a new
         registration statement relating to the securities offered therein, and
         the offering of such securities at that time shall be deemed to be the
         initial bona fide offering thereof.

(c)      Insofar as indemnification for liabilities arising under the Securities
         Act of 1933 may be permitted to directors, officers and controlling
         persons of the Registrant pursuant to the foregoing provisions, or
         otherwise, the Registrant has been advised that in the opinion of the
         Securities and Exchange Commission such indemnification is against
         public policy as expressed in the Act and is, therefore, unenforceable.
         In the event that a claim for indemnification against such liabilities
         (other than the payment by the Registrant of expenses incurred or paid
         by a director, officer or controlling person of the Registrant in the
         successful defense of any action, suit or proceeding) is asserted by
         such director, officer or controlling person in connection with the
         securities being registered, the Registrant will, unless in the opinion
         of its counsel the matter has been settled by controlling precedent,
         submit to a court of appropriate jurisdiction the question whether such
         indemnification by it is against public policy as expressed in the Act
         and will be governed by the final adjudication of such issue.


                                      II-5


<PAGE>


                                   SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, the
Registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in Cambridge, MA, on July 23, 2001.

                                VERTEX PHARMACEUTICALS INCORPORATED



                                BY:  /s/ JOSHUA S. BOGER
                                --------------------------------------------
                                Name:  Joshua S. Boger
                                Title: President and Chief Executive Officer


         Each person whose signature appears below constitutes and appoints
Joshua S. Boger and Sarah P. Cecil, and each of them singly, his true and lawful
attorneys-in-fact and agents, with full power of substitution and resubstitution
in each of them, for him and in his name, place and stead, and in any and all
capacities, to sign any and all amendments (including post-effective amendments)
to this Registration Statement on Form S-8 of Vertex Pharmaceuticals
Incorporated and to file the same, with all exhibits thereto and other documents
in connection therewith, with the Securities and Exchange Commission, granting
unto said attorneys-in-fact and agents, and each of them, full power and
authority to do and perform each and every act and thing requisite or necessary
to be done in or about the premises, as full to all intents and purposes as he
might or could do in person, hereby ratifying and confirming all that said
attorneys-in-fact and agents or any of them or their or his substitute or
substitutes may lawfully do or cause to be done by virtue hereof.

         Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>

             SIGNATURE                                      TITLE                               DATE
<S>                                       <C>                                              <C>

/s/ Joshua S. Boger
-------------------------------               Director, Chairman and Chief                  July 23, 2001
Joshua S. Boger                               Executive Officer (principal
                                              executive officer)

/s/ Johanna Messina Power
-------------------------------               Controller (principal financial               July 23, 2001
Johanna Messina Power                         and accounting officer)


/s/ Barry M. Bloom
-------------------------------               Director                                      July 23, 2001
Barry M. Bloom
</TABLE>

                                      II-6

<PAGE>

<TABLE>
<CAPTION>

             SIGNATURE                                      TITLE                               DATE
<S>                                       <C>                                               <C>


/s/ Roger W. Brimblecombe
-------------------------------               Director                                      July 23, 2001
Roger W. Brimblecombe


/s/ Stuart J.M. Collinson
-------------------------------               Director                                      July 23, 2001
Stuart J.M. Collinson


/s/ Donald R. Conklin
-------------------------------               Director                                      July 23, 2001
Donald R. Conklin


/s/ Bruce I. Sachs
-------------------------------               Director                                      July 23, 2001
Bruce I. Sachs


/s/ Charles A. Sanders
-------------------------------               Director                                      July 23, 2001
Charles A. Sanders


/s/ Elaine S. Ullian
-------------------------------               Director                                      July 23, 2001
Elaine S. Ullian
</TABLE>


                                      II-7

<PAGE>


                       VERTEX PHARMACEUTICALS INCORPORATED

                          INDEX TO EXHIBITS FILED WITH
                         FORM S-8 REGISTRATION STATEMENT


EXHIBIT
NUMBER              DESCRIPTION
-------             -----------

4.1      Specimen Common Stock Certificate (Filed as Exhibit 4.1 to the
         Registrant's Registration Statement on Form S-1 (Registration No.
         33-40966) or amendments thereto and incorporated herein by reference).

4.2      Restated Articles of Organization filed with the Commonwealth of
         Massachusetts on July 31, 1991 (Filed as Exhibit 3.1 to the
         Registrant's Registration Statement on Form S-4 (Reg. No. 333-61480)
         filed on May 23, 2001, and incorporated herein by reference).

4.3      By-Laws, as amended and restated as of March 12, 2001 (Filed as Exhibit
         3.5 to the Registrant's Registration Statement on Form S-4 (Reg. No.
         333-61480) filed on May 23, 2001, and incorporated herein by
         reference).

5        Opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. as to
         the legality of shares being registered.

23.1     Consent of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
         (included in opinion of counsel filed as Exhibit 5).

23.2     Consent of PricewaterhouseCoopers LLP, Independent Accountants.

23.3     Consent of Ernst & Young LLP, Independent Auditors.

23.4     Consent of Arthur Andersen LLP.

23.5     Consent of KPMG LLP.

24       Power of Attorney to file future amendments (set forth on the signature
         page of this Registration Statement.)

99.1     Aurora Biosciences Corporation 1996 Stock Plan, as amended.

99.2     Aurora Biosciences Corporation Employee Stock Purchase Plan, as
         amended, and related offering document.

99.3     1993 Stock Option Plan of PanVera Corporation.

99.4     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Ute Muh.

99.5     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Douglas John Bartels.

99.6     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Steve C. Winans, Ph.D.

99.7     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Michael J. Welsh, M.D.

                                      II-8


<PAGE>


99.8     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Paul V. Dunlap, Ph.D.

99.9     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         J. Woodland Hastings.

99.10    Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Ute Muh, Ph.D.

99.11    Stock Option Agreement between Quorum Sciences, Inc. and James A.
         Romesser, Ph.D.


                                      II-9
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As filed with the Securities and Exchange Commission on July 23, 2001

                                                   REGISTRATION NO. 333-

===============================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                              ---------------------

                                    FORM S-8
                             REGISTRATION STATEMENT
                                    UNDER THE
                             SECURITIES ACT OF 1933

                              ---------------------

                       VERTEX PHARMACEUTICALS INCORPORATED
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

       MASSACHUSETTS                                            04-3039129
(STATE OR OTHER JURISDICTION                                 (I.R.S. EMPLOYER
OF INCORPORATION OR ORGANIZATION)                           IDENTIFICATION NO.)

                               130 WAVERLY STREET
                            CAMBRIDGE, MA 02139-4242
                    (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)

                 AURORA BIOSCIENCES CORPORATION 1996 STOCK PLAN

           AURORA BIOSCIENCES CORPORATION EMPLOYEE STOCK PURCHASE PLAN

                  1993 STOCK OPTION PLAN OF PANVERA CORPORATION

  NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND UTE MUH

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                              DOUGLAS JOHN BARTELS

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                             STEVE C. WINANS, PH.D.

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                             MICHAEL J. WELSH, M.D.

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                              PAUL V. DUNLAP, PH.D.

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                              J. WOODLAND HASTINGS

      NONQUALIFIED STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                                 UTE MUH, PH.D.

            STOCK OPTION AGREEMENT BETWEEN QUORUM SCIENCES, INC. AND
                            JAMES A. ROMESSER, PH.D.
                           (FULL TITLES OF THE PLANS)

                JOSHUA BOGER, PRESIDENT & CHIEF EXECUTIVE OFFICER
                       VERTEX PHARMACEUTICALS INCORPORATED
                               130 WAVERLY STREET
                            CAMBRIDGE, MA 02139-4242

                                 (617) 577-6000
    (NAME, ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER, INCLUDING AREA
                           CODE, OF AGENT FOR SERVICE)

                              ---------------------

                         CALCULATION OF REGISTRATION FEE
============================================================================================================================
                                                              Proposed               Proposed
                                                               maximum                maximum
           Title of                   Amount to be         offering price            aggregate               Amount of
 securities to be registered         registered(1)          per share(2)          offering price(2)     registration fee(3)
----------------------------------------------------------------------------------------------------------------------------
Common Stock, $.01 par value       2,757,632 shares           $14.10                $38,882,611              $ 9,721
                                      310,062 shares           $39.28                $12,179,236              $ 3,045
                                    ---------                                                                 -------
                                    3,067,694 shares                                                          $12,766
                                                                                                              $(2,912)
                                                                                                              $ 9,854
----------------------------------------------------------------------------------------------------------------------------
 Rights to Purchase Series A             (4)                    (4)                    (4)                     None
     Junior Participating
       Preferred Stock
============================================================================================================================
(1)      The number of shares of Common Stock, par value $.01 per share ("Common
         Stock"), stated above consists of the aggregate number of shares which
         may be sold (i) upon exercise of options which have been granted under
         the Aurora Biosciences Corporation 1996 Stock Plan, 1993 Stock Option
         Plan of PanVera Corporation and Option Agreements between Quorum
         Sciences, Inc. and certain of its employees and shares of stock which
         may hereafter be sold under the Aurora Biosciences Corporation Employee
         Stock Purchase Plan (collectively, the "Plans"). The maximum number of
         shares which may be sold upon exercise of options granted under the
         Plans are subject to adjustment in accordance with certain
         anti-dilution and other provisions of the Plans. Accordingly, pursuant
         to Rule 416 under the Securities Act of 1933, as amended (the
         "Securities Act"), this Registration Statement covers, in addition to
         the number of shares stated above, an indeterminate number of shares
         which may be subject to grant or otherwise issuable after the operation
         of any such anti-dilution and other provisions.

(2)      Estimated solely for the purpose of determining the registration fee in
         accordance with Rule 457(c) and (h) under the Securities Act of 1933,
         as amended, as follows: (i) in the case of shares of Common Stock which
         may be purchased on the exercise of outstanding options, the fee is
         calculated based on the weighted average exercise price of the
         outstanding options; and (ii) in the case of shares of Common Stock
         which may be purchased under the Aurora Biosciences Corporation
         Employee Stock Purchase Plan, the price of which is unknown, the fee is
         calculated on the basis of the average high and low sales prices per
         share of the Common Stock on The Nasdaq National Market of $39.28 on
         July 18, 2001 within 5 business days prior to filing this registration
         statement.

(3)      Pursuant to Rule 457, the Registrant prepaid the registration fee for
         586,977 shares under the Plans when it registered up to 14,725,000
         shares of Common Stock pursuant to Registration Statement on Form S-4
         (File Number 333-61480) initially filed on May 23, 2001. Therefore,
         $2,912 is offset against the total currently due filing fee of
         $12,766.

(4)      No separate consideration will be received for the Rights.

===============================================================================
EXPLANATORY NOTE

         Vertex Pharmaceuticals Incorporated (the "Registrant") hereby files
this Registration Statement on Form S-8 relating to its Common Stock, par value
$0.01 per share, which may be sold upon the exercise of options granted: (i)
under the Aurora Biosciences Corporation ("Aurora") 1996 Stock Plan, (ii) under
the Aurora Employee Stock Purchase Plan, (iii) under the 1993 Stock Option Plan
of PanVera Corporation and (iv) under the Stock Option Agreements between Quorum
Sciences, Inc. and certain of its employees (collectively the "Plans").

         Pursuant to the merger (the "Merger") provided for in the Agreement
and Plan of Merger, dated as of April 29, 2001, among the Registrant, Aurora
and Ahab Acquisition Sub, Inc. ("Ahab Sub"), a wholly owned subsidiary of the
Registrant, Ahab Sub was merged into Aurora and Aurora became a wholly owned
subsidiary of the Registrant effective July 18, 2001. Upon consummation of
the Merger, the Registrant assumed the obligations of Aurora under the Plans
and each option is governed by the same terms and conditions that governed
the applicable option immediately prior to the Merger except that:

         o        each such option is exercisable for the number of shares
                  of the Registrant's common stock equal to the number of shares
                  of Aurora common stock issuable upon exercise of the option
                  multiplied by 0.62, rounded down to the nearest whole share;

         o        the per share exercise price for the shares of the
                  Registrant's common stock issuable upon the exercise of the
                  assumed option is equal to the exercise price per share
                  of the Aurora option divided by 0.62, rounded up to the
                  nearest whole cent; and

         o        each outstanding restricted share of Aurora common stock was
                  converted into the number of restricted shares of the
                  Registrant's Common Stock that is equal to the product of 0.62
                  multiplied by the shares of Aurora common stock subject to the
                  award.

         This Registration Statement relates to the Common Stock of the
Registrant issuable upon exercise of the options or which may be sold pursuant
to the Plans as follows:

         o        2,616,985 shares subject to the Aurora 1996 Stock Plan.

         o        310,062 shares subject to the Aurora Employee Stock Purchase
                  Plan.

         o        137,947 shares subject to the 1993 Stock Option Plan of
                  PanVera Corporation.

         o        2,700 shares subject to the Stock Option Agreements between
                  Quorum Sciences, Inc. and certain of its employees.
PART I

         In accordance with the instructional Note to Part I of Form S-8 as
promulgated by the Securities and Exchange Commission, the information specified
by Part I of Form S-8 has been omitted from this Registration Statement on Form
S-8 for offers of Common Stock pursuant to the Aurora 1996 Stock Plan, the
Aurora Employee Stock Purchase Plan, the 1993 Stock Option Plan of PanVera
Corporation, and the Stock Option Agreements between Quorum Sciences, Inc. and
certain of its employees.

                                      I-1
PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.  INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE.

         The following documents filed by the Registrant or Aurora Biosciences
Corporation with the Commission are incorporated herein by reference:

         (a) The Registrant's Annual Report on Form 10-K for the fiscal year
ended December 31, 2000 (filing date March 26, 2001).

         (b) The Registrant's Quarterly Report on Form 10-Q (Commission File No.
000-19319) for the quarter ended March 31, 2001 (filing date May 15, 2001).

         (c) The Registrant's Current Report on Form 8-K for the April 29, 2001
event (filing date April 30, 2001).

         (d) Aurora's Annual Report on Form 10-K for the fiscal year ended
December 31, 2000 (filing date March 15, 2001).

         (e) Aurora's Quarterly Report on Form 10-Q for the quarterly period
ended March 31, 2001 (filing date May 11, 2001).

         (f) Aurora's Current Report on Form 8-K for the February 7, 2001 event
(filing date February 7, 2001).

         (g) Aurora's Current Report on Form 8-K for the March 1, 2001 event
(filing date March 7, 2001).

         (h) Aurora's Current Report on Form 8-K for the April 2, 2001 event
(filing date April 5, 2001).

         (i) Aurora's Current Report on Form 8-K for the April 29, 2001 event
(filing date April 30, 2001).

         (j) Aurora's Current Report on Form 8-K for the March 1, 2001 event
(filing date May 18, 2001), which contains financial statements and related
information that restate and supercede the financial statements and related
information in Aurora's Annual Report on Form 10-K for the fiscal year ended
December 31, 2000, filed on March 15, 2001.

         (k) Description of the Registrant's Common Stock included in the
Registrant's Registration Statement on Form S-4 (Reg. No. 333-61480) filed under
the Securities Act of 1933, including any amendment or report filed for the
purpose of updating such description.

         All reports and other documents filed by the Registrant after the date
hereof pursuant to Sections 13(a), 13(c), 14 and 15(d) of the Securities
Exchange Act of 1934 prior to the filing of a post-effective amendment which
indicates that all securities offered hereby have been sold or which deregisters

                                      II-1
all securities then remaining unsold, shall be deemed to be incorporated by
reference herein and to be part hereof from the date of filing of such reports
and documents.

ITEM 4.  DESCRIPTION OF SECURITIES.

         Not applicable.

ITEM 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL.

         Not applicable.

ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

         Part D of Article 6 of the Restated Articles of Organization of the
Registrant provides that no director of the Registrant shall be personally
liable to the Registrant or its stockholders for monetary damages for breach of
fiduciary duty as a director. Such paragraph provides further, however, that, to
the extent provided by applicable law, it will not eliminate or limit the
liability of a director (i) for any breach of the director's duty of loyalty to
the Registrant or its stockholders, (ii) for acts or omissions not in good faith
or which involve intentional misconduct or a knowing violation of law, (iii) for
distributions made in violation of the Registrant's Restated Articles of
Organization or which are made when the Registrant is insolvent or which renders
it insolvent, (iv) for loans made to officers or directors of the Registrant
which are not repaid if the director has voted for such loans and they have not
been approved or ratified as loans reasonably expected to benefit the
Registrant, by a majority of directors who are not recipients of such loans or
the holders of a majority of voting shares, which holders are not recipients of
such loans, and (v) for any transactions from which the director derived an
improper personal benefit.

         Article V of the Registrant's By-laws provides that the Registrant
shall indemnify each of its directors and officers (including persons who serve
at the Registrant's request as a director, officer or trustee of another
organization in which the Registrant has any interest, direct or indirect, as a
stockholder, creditor or otherwise or who serve at the Registrant's request in
any capacity with respect to any employee benefit plan) against all liabilities
and expenses, including amounts paid in satisfaction of judgments, in compromise
or as fines and penalties and counsel fees reasonably incurred by such director
or officer in connection with the defense or disposition of any action, suit or
other proceeding, whether civil or criminal, in which such director or officer
may be involved or with which such person may be threatened, while in office or
thereafter, by reason of such person's being or having been such a director,
officer or trustee, except with respect to any matter as to which such director
or officer shall have been adjudicated in any proceeding not to have acted in
good faith in the reasonable belief that such director's or officer's action was
in the best interest of the Registrant or, to the extent that such matter
relates to service with respect to an employee benefit plan, in the best
interest of the participants or beneficiaries of such employee benefit plan.

         As to any matter disposed of by a compromise payment by any such
person, pursuant to a consent decree or otherwise, Article V of the Registrant's
By-laws provides that no indemnification shall be provided to such person for
such payment or for any other expenses unless such compromise has been approved
as in the best interest of the Registrant, after notice that it involves such
indemnification (i) by a disinterested majority of the directors then in office,
(ii) by a majority of the disinterested directors then in office, provided there
has been obtained an opinion in writing of independent legal counsel to the
effect

                                      II-2
that such director or officer appears to have acted in good faith in the
reasonable belief that such person's action was in the best interest of the
Registrant, or (iii) by the holders of a majority of the outstanding stock at
the time entitled to vote for directors, voting as a single class, exclusive of
any stock owned by any interested director or officer.

         Article V of the Registrant's By-laws provides that expenses, including
counsel fees, reasonably incurred by any director or officer in connection with
the defense or disposition of any such action, suit or other proceeding may be
paid from time to time by the Registrant at the discretion of a majority of the
disinterested directors then in office, in advance of the final disposition
thereof, upon receipt of an undertaking by such director or officer to repay the
Registrant the amounts so paid if it is ultimately determined that
indemnification for such expenses is not authorized under Article V of the
By-laws, which undertaking may be accepted by the Registrant without reference
to the financial ability of such director or officer to make repayment.

         Article V of the Registrant's By-laws gives the Board of Directors of
the Registrant the power to authorize the purchase and maintenance of insurance,
in such amounts as the Board of Directors may from time to time deem
appropriate, on behalf of any person who is or was a director, officer or agent
of the Registrant, or who is or was serving at the request of the Registrant as
a director, officer or agent of another organization in which the Registrant has
any interest, direct or indirect, as a shareholder, creditor or otherwise, or
with respect to any employee benefit plan, against any liability incurred by
such person in any such capacity, or arising out of such person's status as such
agent, whether or not such person is entitled to indemnification by the
Registrant pursuant to Article V or otherwise and whether or not the Registrant
would have the power to indemnify the person against such liability.

         Section 13(b)(1 1/2) of the Massachusetts Business Corporation Law,
Chapter 156B of the General Laws of Massachusetts (the "MBCL") authorizes the
provisions, described above, contained in Part D of Article 6 of the Restated
Articles of Organization of the Registrant.

         Section 67 of the MBCL authorizes the provisions, described above,
contained in Article V of the By-laws of the Registrant.

         Section 65 of the MBCL provides that performance by a director, officer
or incorporator of such person's duties in good faith and in a manner such
person reasonably believes to be in the best interest of the corporation, and
with such care as an ordinary prudent person in a like position would use under
similar circumstances, shall be a complete defense to any claim asserted against
such director, officer or incorporator, except as otherwise expressly provided
by statute, by reason of such person's being or having been a director, officer
or incorporator of the corporation.

ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED.

         Not applicable.

ITEM 8.  EXHIBITS.

         4.1      Specimen Common Stock Certificate (Filed as Exhibit 4.1 to the
                  Registrant's Registration Statement on Form S-1 (Registration
                  No. 33-40966) or amendments thereto and incorporated herein by
                  reference).

                                      II-3
4.2      Restated Articles of Organization filed with the Commonwealth
                  of Massachusetts on July 31, 1991 (Filed as Exhibit 3.1 to the
                  Registrant's Registration Statement on Form S-4 (Reg. No.
                  333-61480) filed on May 23, 2001, and incorporated herein by
                  reference).

         4.3      By-Laws, as amended and restated as of March 12, 2001 (Filed
                  as Exhibit 3.5 to the Registrant's Registration Statement on
                  Form S-4 (Reg. No. 333-61480) filed on May 23, 2001, and
                  incorporated herein by reference).

         5        Opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
                  as to the legality of shares being registered.

         23.1     Consent of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
                  (included in opinion of counsel filed as Exhibit 5).

         23.2     Consent of PricewaterhouseCoopers LLP, Independent
                  Accountants.

         23.3     Consent of Ernst & Young LLP, Independent Auditors.

         23.4     Consent of Arthur Andersen LLP.

         23.5     Consent of KPMG LLP.

         24       Power of Attorney to file future amendments (set forth on the
                  signature page of this Registration Statement.)

         99.1     Aurora Biosciences Corporation 1996 Stock Plan, as amended.

         99.2     Aurora Biosciences Corporation Employee Stock Purchase Plan,
                  as amended, and related offering document.

         99.3     1993 Stock Option Plan of PanVera Corporation.

         99.4     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Ute Muh.

         99.5     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Douglas John Bartels.

         99.6     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Steve C. Winans, Ph.D.

         99.7     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Michael J. Welsh, M.D.

         99.8     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Paul V. Dunlap, Ph.D.

         99.9     Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and J. Woodland Hastings, Ph.D.

         99.10    Nonqualified Stock Option Agreement between Quorum Sciences,
                  Inc. and Ute Muh, Ph.D.

         99.11    Stock Option Agreement between Quorum Sciences, Inc. and James
                  A. Romesser, Ph.D.

                                      II-4
ITEM 9.  UNDERTAKINGS.

(a)      The undersigned Registrant hereby undertakes:

         (1) To file, during any period in which offers or sales are being made,
         a post-effective amendment to this Registration Statement:

                  (i) To include any prospectus required by Section 10(a)(3) of
                  the Securities Act of 1933;

                  (ii) To reflect in the prospectus any facts or events arising
                  after the effective date of the Registration Statement (or the
                  most recent post-effective amendment thereof) which,
                  individually or in the aggregate, represents a fundamental
                  change in the information set forth in the Registration
                  Statement. Notwithstanding the foregoing, any increase or
                  decrease in volume of securities offered (if the total dollar
                  value of securities offered would not exceed that which was
                  registered) and any deviation from the low or high end of the
                  estimated maximum offering range may be reflected in the form
                  of prospectus filed with the Commission pursuant to Rule
                  424(b) if, in the aggregate, the changes in volume and price
                  represent no more than a 20% change in the maximum aggregate
                  offering price set forth in the "Calculation of Registration
                  Fee" table in the effective Registration Statement.

                  (iii) To include any material information with respect to the
                  plan of distribution not previously disclosed in the
                  Registration Statement or any material change to such
                  information in the Registration Statement;

                           PROVIDED, HOWEVER, that paragraphs (a)(1)(i) and
                  (a)(1)(ii) do not apply if the Registration Statement is on
                  Form S-3, Form S-8 or Form F-3, and the information required
                  to be included in a post-effective amendment by those
                  paragraphs is contained in periodic reports filed with or
                  furnished to the Commission by the Registrant pursuant to
                  Section 13 or Section 15(d) of the Securities Exchange Act of
                  1934 that are incorporated by reference in this Registration
                  Statement.

         (2) That, for the purpose of determining any liability under the
         Securities Act of 1933, each such post-effective amendment shall be
         deemed to be a new registration statement relating to the securities
         offered therein, and the offering of such securities at that time shall
         be deemed to be the initial bona fide offering thereof.

         (3) To remove from registration by means of a post-effective amendment
         any of the securities being registered which remain unsold at the
         termination of the offering.

(b)      The undersigned Registrant hereby undertakes that, for purposes of
         determining any liability under the Securities Act of 1933, each filing
         of the Registrant's annual report pursuant to Section 13(a) or Section
         15(d) of the Securities Exchange Act of 1934 that is incorporated by
         reference in this Registration Statement shall be deemed to be a new
         registration statement relating to the securities offered therein, and
         the offering of such securities at that time shall be deemed to be the
         initial bona fide offering thereof.

(c)      Insofar as indemnification for liabilities arising under the Securities
         Act of 1933 may be permitted to directors, officers and controlling
         persons of the Registrant pursuant to the foregoing provisions, or
         otherwise, the Registrant has been advised that in the opinion of the
         Securities and Exchange Commission such indemnification is against
         public policy as expressed in the Act and is, therefore, unenforceable.
         In the event that a claim for indemnification against such liabilities
         (other than the payment by the Registrant of expenses incurred or paid
         by a director, officer or controlling person of the Registrant in the
         successful defense of any action, suit or proceeding) is asserted by
         such director, officer or controlling person in connection with the
         securities being registered, the Registrant will, unless in the opinion
         of its counsel the matter has been settled by controlling precedent,
         submit to a court of appropriate jurisdiction the question whether such
         indemnification by it is against public policy as expressed in the Act
         and will be governed by the final adjudication of such issue.

                                      II-5
SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, the
Registrant certifies that it has reasonable grounds to believe that it meets all
of the requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in Cambridge, MA, on July 23, 2001.

                                VERTEX PHARMACEUTICALS INCORPORATED

                                BY:  /s/ JOSHUA S. BOGER
                                --------------------------------------------
                                Name:  Joshua S. Boger
                                Title: President and Chief Executive Officer

         Each person whose signature appears below constitutes and appoints
Joshua S. Boger and Sarah P. Cecil, and each of them singly, his true and lawful
attorneys-in-fact and agents, with full power of substitution and resubstitution
in each of them, for him and in his name, place and stead, and in any and all
capacities, to sign any and all amendments (including post-effective amendments)
to this Registration Statement on Form S-8 of Vertex Pharmaceuticals
Incorporated and to file the same, with all exhibits thereto and other documents
in connection therewith, with the Securities and Exchange Commission, granting
unto said attorneys-in-fact and agents, and each of them, full power and
authority to do and perform each and every act and thing requisite or necessary
to be done in or about the premises, as full to all intents and purposes as he
might or could do in person, hereby ratifying and confirming all that said
attorneys-in-fact and agents or any of them or their or his substitute or
substitutes may lawfully do or cause to be done by virtue hereof.

         Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.
SIGNATURE                                      TITLE                               DATE
/s/ Joshua S. Boger
-------------------------------               Director, Chairman and Chief                  July 23, 2001
Joshua S. Boger                               Executive Officer (principal
                                              executive officer)

/s/ Johanna Messina Power
-------------------------------               Controller (principal financial               July 23, 2001
Johanna Messina Power                         and accounting officer)

/s/ Barry M. Bloom
-------------------------------               Director                                      July 23, 2001
Barry M. Bloom
II-6
SIGNATURE                                      TITLE                               DATE
/s/ Roger W. Brimblecombe
-------------------------------               Director                                      July 23, 2001
Roger W. Brimblecombe

/s/ Stuart J.M. Collinson
-------------------------------               Director                                      July 23, 2001
Stuart J.M. Collinson

/s/ Donald R. Conklin
-------------------------------               Director                                      July 23, 2001
Donald R. Conklin

/s/ Bruce I. Sachs
-------------------------------               Director                                      July 23, 2001
Bruce I. Sachs

/s/ Charles A. Sanders
-------------------------------               Director                                      July 23, 2001
Charles A. Sanders

/s/ Elaine S. Ullian
-------------------------------               Director                                      July 23, 2001
Elaine S. Ullian
II-7
VERTEX PHARMACEUTICALS INCORPORATED

                          INDEX TO EXHIBITS FILED WITH
                         FORM S-8 REGISTRATION STATEMENT

EXHIBIT
NUMBER              DESCRIPTION
-------             -----------

4.1      Specimen Common Stock Certificate (Filed as Exhibit 4.1 to the
         Registrant's Registration Statement on Form S-1 (Registration No.
         33-40966) or amendments thereto and incorporated herein by reference).

4.2      Restated Articles of Organization filed with the Commonwealth of
         Massachusetts on July 31, 1991 (Filed as Exhibit 3.1 to the
         Registrant's Registration Statement on Form S-4 (Reg. No. 333-61480)
         filed on May 23, 2001, and incorporated herein by reference).

4.3      By-Laws, as amended and restated as of March 12, 2001 (Filed as Exhibit
         3.5 to the Registrant's Registration Statement on Form S-4 (Reg. No.
         333-61480) filed on May 23, 2001, and incorporated herein by
         reference).

5        Opinion of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. as to
         the legality of shares being registered.

23.1     Consent of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C.
         (included in opinion of counsel filed as Exhibit 5).

23.2     Consent of PricewaterhouseCoopers LLP, Independent Accountants.

23.3     Consent of Ernst & Young LLP, Independent Auditors.

23.4     Consent of Arthur Andersen LLP.

23.5     Consent of KPMG LLP.

24       Power of Attorney to file future amendments (set forth on the signature
         page of this Registration Statement.)

99.1     Aurora Biosciences Corporation 1996 Stock Plan, as amended.

99.2     Aurora Biosciences Corporation Employee Stock Purchase Plan, as
         amended, and related offering document.

99.3     1993 Stock Option Plan of PanVera Corporation.

99.4     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Ute Muh.

99.5     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Douglas John Bartels.

99.6     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Steve C. Winans, Ph.D.

99.7     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Michael J. Welsh, M.D.

                                      II-8
99.8     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Paul V. Dunlap, Ph.D.

99.9     Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         J. Woodland Hastings.

99.10    Nonqualified Stock Option Agreement between Quorum Sciences, Inc. and
         Ute Muh, Ph.D.

99.11    Stock Option Agreement between Quorum Sciences, Inc. and James A.
         Romesser, Ph.D.

                                      II-9