<PAGE>

AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MAY 3, 2001
                                                   FILE NO. 333-______


                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


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


                          CUBIST PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)


           DELAWARE                                            22-3192085
(STATE OR OTHER JURISDICTION OF                             (I.R.S. EMPLOYER
INCORPORATION OR ORGANIZATION)                             IDENTIFICATION NO.)


                      24 EMILY STREET, CAMBRIDGE, MA 02139
               (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES) (ZIP CODE)


                          CUBIST PHARMACEUTICALS, INC.
                    2000 NONSTATUTORY STOCK OPTION PLAN AND
                          CUBIST PHARMACEUTICALS, INC.
                           2001 UK STOCK OPTION PLAN
                            (FULL TITLE OF THE PLAN)


                            SCOTT M. ROCKLAGE, PH.D.
    Chairman of the Board of Directors, President and Chief Executive Officer
                          CUBIST PHARMACEUTICALS, INC.
                                 24 Emily Street
                         Cambridge, Massachusetts 02139
                     (NAME AND ADDRESS OF AGENT FOR SERVICE)

                                 (617) 576-1999
           TELEPHONE NUMBER, INCLUDING AREA CODE, OF AGENT FOR SERVICE


                                   COPIES TO:

                               JULIO E. VEGA, ESQ.
                            MATTHEW J. CUSHING, ESQ.
                                BINGHAM DANA LLP
                               150 Federal Street
                              Boston, MA 02110-1726
                                 (617) 951-8000

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>

=================================================================================================================
                                                            PROPOSED           PROPOSED
                                          AMOUNT            MAXIMUM            MAXIMUM             AMOUNT OF
           TITLE OF                       TO BE          OFFERING PRICE        AGGREGATE          REGISTRATION
  SECURITIES TO BE REGISTERED           REGISTERED          PER SHARE       OFFERING PRICE            FEE
-----------------------------------------------------------------------------------------------------------------
<S>                                      <C>                <C>               <C>                 <C>
Common Stock,
$0.001 par value.................        1,500,000          $28.39 (1)        $42,585,000(1)      $10,646.25
=================================================================================================================
</TABLE>

(1) The proposed maximum offering price has been estimated pursuant to Rule
457(h) solely for the purpose of calculating the registration fee. It is not
known how many of these shares will be purchased or at what price. The
estimate of the proposed maximum aggregate offering price has been calculated
based on the offering of all 1,500,000 shares registered hereunder pursuant
to the grant of stock options under the Plans exercisable for all of such
shares, at an exercise price of $28.39 per share, which is the average of the
high and low prices of the Registrant's Common Stock as listed on the
National Association of Securities Dealers Automated Quotation ("Nasdaq")
National Market System on April 26, 2001.

Pursuant to Rule 429 promulgated under the Securities Act of 1933, as
amended, the Prospectus relating to this Registration Statement is a combined
Prospectus that relates also to the Registration Statement on Form S-8 (File
No. 333-60152) previously filed by the Registrant on May 3, 2001, which
registers 1,080,359 shares of Common Stock, Registration Statement on Form
S-8 (File No. 333-49522) previously filed by the Registrant on November 8,
2000, which registers 1,000,000 shares of Common Stock, Registration
Statement on Form S-8 (File No. 333-32178) previously filed by the Registrant
on March 10, 2000, which registers 844,573 shares of Common Stock, the
Registration Statement on Form S-8 (File No. 333-65385) previously filed by
the Registrant on October 6, 1998, which registers 655,427 shares of Common
Stock, and the Registration Statement on Form S-8 (File No. 33-25707)
previously filed by the Registrant on April 23, 1997, which registers
1,500,000 shares of Common Stock. A filing fee in the amount of $33,627.14
was previously paid with respect to such shares.

<PAGE>

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE.

         We incorporate by reference the documents listed below and any future
filings we will make with the SEC under Section 13(a), 13(c), 14 or 15(d) of the
Securities Exchange Act of 1934:

         --       Annual Report on Form 10-K for the year ended December 31,
                  2000, filed on April 2, 2001;

         --       the description of our common stock contained in our
                  registration statement on Form 8-A filed with the SEC on
                  September 17, 1996, including any amendments or reports filed
                  for the purpose of updating that description; and

         --       the description of the preferred stock purchase rights for our
                  Series A Junior Participating Preferred Stock contained in our
                  registration statement on Form 8-A filed with the SEC on
                  August 2, 1999, including any amendments or reports filed for
                  the purpose of updating that description.

         You may request a copy of these filings at no cost (other than exhibits
unless those exhibits are specifically incorporated by reference herein) by
writing, telephoning or e-mailing us at the following address:

                             Cubist Pharmaceuticals, Inc.
                             24 Emily Street
                             Cambridge, MA 02139
                             Attn: Thomas A. Shea
                             (617) 576-1999
                             e-mail: tshea@cubist.com

ITEM 4.  DESCRIPTION OF SECURITIES

         Not applicable.


ITEM 5.  INTERESTS OF NAMED EXPERTS OR COUNSEL

         Not applicable.


ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

         Section 145 of the Delaware General Corporation Law empowers a Delaware
corporation to indemnify its officers and directors and certain other persons to
the extent and under the circumstances set forth therein.

         The Restated Certificate of Incorporation and the Amended and Restated
By-Laws of the Company, copies of which are filed herein as Exhibits 3.1 and
3.2, provide for advancement of expenses and indemnification of officers and
directors of the Registrant and certain other persons against liabilities and

<PAGE>


expenses incurred by any of them in certain stated proceedings and under certain
stated conditions to the fullest extent permissible under Delaware law.

         The Company intends to maintain insurance for the benefit of its
directors and officers insuring such persons against certain liabilities,
including liabilities under the securities laws.

ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED

         Not applicable.

ITEM 8.  EXHIBITS

         The following exhibits are filed as part of this Registration
Statement:

         3.1      Restated Certificate of Incorporation of the Registrant
                  (incorporated by reference to Exhibit 3 to Cubist's Quarterly
                  Report on Form 10-Q filed on August 12, 1999) (File no.
                  000-21379).

         3.2      Amended and Restated By-Laws of the Registrant, as amended to
                  date. (incorporated by reference to Exhibit 3.4, Registration
                  No. 333-6795).

         4.1      Specimen certificate for shares of Common Stock (incorporated
                  by reference to Exhibit 3.4 to Cubist's Registration Statement
                  on Form S-1) (Registration No. 333-6795).

         4.2      Rights Agreement dated as of July 21, 1999 between Cubist and
                  BankBoston, N.A. as Rights Agent (incorporated by reference to
                  Exhibit 99.1 to Cubist's Report on Form 8-K filed on July 30,
                  1999) (File no. 000-21379).

         4.3      First Amendment, dated as of March 7, 2000, to the Rights
                  Agreement, dated as of July 21, 2000 between the Company and
                  Fleet National Bank f/k/a BankBoston, N.A., as Rights Agent
                  (incorporated herein by reference to Exhibit 4.2 to the
                  Company's Registration Statement on Form 8-A/A filed on March
                  9, 2000) (File No. 000-21379).

         4.4      Form of Amended Rights Certificate (incorporated herein by
                  reference to Exhibit 4.4 to the Company's Registration
                  Statement on Form 8-A/A filed on March 9, 2000) (File No.
                  000-21379).

         5        Opinion and Consent of Bingham Dana LLP with respect to the
                  legality of the shares being registered.

         23.1     Consent of Bingham Dana LLP (included in Exhibit 5).

         23.3     Consent of KPMG LLP.

         23.2     Consent of PricewaterhouseCoopers LLP.

         24       Power of Attorney (included in signature page to Registration
                  Statement).

ITEM 9.  UNDERTAKINGS

         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 to include any
         material information with respect to the plan of distribution not


                                       2
<PAGE>


         previously disclosed in this Registration Statement or any material
         change to such information in this Registration Statement;

(2)      That, for the purpose of determining any liability under the Securities
         Act of 1933, as amended (the "SECURITIES ACT"), 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;

(4)      That, for purposes of determining any liability under the Securities
         Act, each filing of the Registrant's annual report pursuant to Section
         13(a) or 15(d) of the Exchange Act (and, where applicable, each filing
         of an employee benefit plan's annual report pursuant to Section 15(d)
         of the Exchange Act) that is incorporated by reference in the
         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; and

(5)      Insofar as indemnification for liabilities arising under the Securities
         Act 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 SEC such
         indemnification is against public policy as expressed in the Securities
         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 Securities Act and will
         be governed by the final adjudication of such issue.


                                       3
<PAGE>


                                   SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, as amended,
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 the City of Cambridge, Commonwealth of Massachusetts, on
this 30th day of April, 2001.

                              CUBIST PHARMACEUTICALS, INC.


                              By: /s/ Scott M. Rocklage
                                  -------------------------------------
                                  Scott M. Rocklage, Ph.D.
                                  Chairman of the Board of Directors,
                                  President and Chief Executive Officer


                                POWER OF ATTORNEY

         Each person whose signature appears below hereby appoints Scott M.
Rocklage and Thomas A. Shea and each of them severally, acting alone and without
the other, his/her true and lawful attorney-in-fact with the authority to
execute in the name of each such person, and to file with the Securities and
Exchange Commission, together with any exhibits thereto and other documents
therewith, any and all amendments (including without limitation post-effective
amendments) to this Registration Statement on Form S-8 necessary or advisable to
enable the Registrant to comply with the Securities Act of 1933, as amended, and
any rules, regulations, and requirements of the Securities and Exchange
Commission in respect thereof, which amendments may make such other changes in
the Registration Statement as the aforesaid attorney-in-fact executing the same
deems appropriate.

         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 date indicated.

<TABLE>
<CAPTION>

            SIGNATURE                                       TITLE                                     DATE
<S>                                      <C>                                                   <C>
/s/ Scott M. Rocklage                    Chairman of the Board of Directors, President,        April 30, 2001
------------------------------------     Chief Executive Officer and Director
Scott M. Rocklage                        (Principal Executive Officer)

/s/ Thomas A. Shea                       Vice President and Chief Financial Officer             April 30, 2001
------------------------------------
Thomas A. Shea

/s/ Susan Bayh                           Director                                               April 30, 2001
------------------------------------
Susan Bayh

/s/ Barry M. Bloom                       Director                                               April 30, 2001
------------------------------------
Barry M. Bloom

/s/ John K. Clarke                       Director                                               April 30, 2001
------------------------------------
John K. Clarke

/s/ David Martin                         Director                                               April 30, 2001
------------------------------------
David Martin

/s/ Walter Maupay                        Director                                               April 30, 2001
------------------------------------
Walter Maupay

/s/ Paul R. Schimmel                     Director                                               April 30, 2001
------------------------------------
Paul R. Schimmel

/s/ John Zabriskie                       Director                                               April 30, 2001
------------------------------------
John Zabriskie

</TABLE>

<PAGE>


                                INDEX TO EXHIBITS

EXHIBIT
NUMBER                            DESCRIPTION

3.1      Restated Certificate of Incorporation of the Registrant (incorporated
         by reference to Exhibit 3 to Cubist's Quarterly Report on Form 10-Q
         filed on August 12, 1999) (File no. 000-21379).

3.2      Amended and Restated By-Laws of the Registrant, as amended to date.
         (incorporated by reference to Exhibit 3.4, Registration No. 333-6795).

4.1      Specimen certificate for shares of Common Stock (incorporated by
         reference to Exhibit 3.4 to Cubist's Registration Statement on Form
         S-1) (Registration No. 333-6795).

4.2      Rights Agreement dated as of July 21, 1999 between Cubist and
         BankBoston, N.A. as Rights Agent (incorporated by reference to Exhibit
         99.1 to Cubist's Report on Form 8-K filed on July 30, 1999) (File no.
         000-21379).

4.3      First Amendment, dated as of March 7, 2000, to the Rights Agreement,
         dated as of July 21, 2000 between the Company and Fleet National Bank
         f/k/a BankBoston, N.A., as Rights Agent (incorporated herein by
         reference to Exhibit 4.2 to the Company's Registration Statement on
         Form 8-A/A filed on March 9, 2000) (File No. 000-21379)

4.4      Form of Amended Rights Certificate (incorporated herein by reference to
         Exhibit 4.4 to the Company's Registration Statement on Form 8-A/A filed
         on March 9, 2000) (File No. 000-21379)

5        Opinion and Consent of Bingham Dana LLP with respect to the legality of
         the shares being registered.

23.1     Consent of Bingham Dana LLP (included in Exhibit 5).

23.2     Consent of PricewaterhouseCoopers LLP.

23.3     Consent of KPMG LLP.

24       Power of Attorney (included in signature page to Registration
         Statement).
[{"type": "S-8", "sequence": "1", "filename": "a2043444zs-8.txt", "description": "S-8", "secsgml_size_bytes": 18605}]
{"company-data": {"conformed-name": "CUBIST PHARMACEUTICALS INC", "cik": "0000912183", "assigned-sic": "2834", "irs-number": "223192085", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-60168", "film-number": "1621764"}, "business-address": {"street1": "24 EMILY ST", "city": "CAMBRIDGE", "state": "MA", "zip": "02139", "phone": "6075761999"}, "mail-address": {"street1": "24 EMILY ST", "city": "CAMBRIDGE", "state": "MA", "zip": "02139"}}
AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON MAY 3, 2001
                                                   FILE NO. 333-______

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

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

                          CUBIST PHARMACEUTICALS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

           DELAWARE                                            22-3192085
(STATE OR OTHER JURISDICTION OF                             (I.R.S. EMPLOYER
INCORPORATION OR ORGANIZATION)                             IDENTIFICATION NO.)

                      24 EMILY STREET, CAMBRIDGE, MA 02139
               (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES) (ZIP CODE)

                          CUBIST PHARMACEUTICALS, INC.
                    2000 NONSTATUTORY STOCK OPTION PLAN AND
                          CUBIST PHARMACEUTICALS, INC.
                           2001 UK STOCK OPTION PLAN
                            (FULL TITLE OF THE PLAN)

                            SCOTT M. ROCKLAGE, PH.D.
    Chairman of the Board of Directors, President and Chief Executive Officer
                          CUBIST PHARMACEUTICALS, INC.
                                 24 Emily Street
                         Cambridge, Massachusetts 02139
                     (NAME AND ADDRESS OF AGENT FOR SERVICE)

                                 (617) 576-1999
           TELEPHONE NUMBER, INCLUDING AREA CODE, OF AGENT FOR SERVICE

                                   COPIES TO:

                               JULIO E. VEGA, ESQ.
                            MATTHEW J. CUSHING, ESQ.
                                BINGHAM DANA LLP
                               150 Federal Street
                              Boston, MA 02110-1726
                                 (617) 951-8000

                         CALCULATION OF REGISTRATION FEE
=================================================================================================================
                                                            PROPOSED           PROPOSED
                                          AMOUNT            MAXIMUM            MAXIMUM             AMOUNT OF
           TITLE OF                       TO BE          OFFERING PRICE        AGGREGATE          REGISTRATION
  SECURITIES TO BE REGISTERED           REGISTERED          PER SHARE       OFFERING PRICE            FEE
-----------------------------------------------------------------------------------------------------------------
Common Stock,
$0.001 par value.................        1,500,000          $28.39 (1)        $42,585,000(1)      $10,646.25
=================================================================================================================
(1) The proposed maximum offering price has been estimated pursuant to Rule
457(h) solely for the purpose of calculating the registration fee. It is not
known how many of these shares will be purchased or at what price. The
estimate of the proposed maximum aggregate offering price has been calculated
based on the offering of all 1,500,000 shares registered hereunder pursuant
to the grant of stock options under the Plans exercisable for all of such
shares, at an exercise price of $28.39 per share, which is the average of the
high and low prices of the Registrant's Common Stock as listed on the
National Association of Securities Dealers Automated Quotation ("Nasdaq")
National Market System on April 26, 2001.

Pursuant to Rule 429 promulgated under the Securities Act of 1933, as
amended, the Prospectus relating to this Registration Statement is a combined
Prospectus that relates also to the Registration Statement on Form S-8 (File
No. 333-60152) previously filed by the Registrant on May 3, 2001, which
registers 1,080,359 shares of Common Stock, Registration Statement on Form
S-8 (File No. 333-49522) previously filed by the Registrant on November 8,
2000, which registers 1,000,000 shares of Common Stock, Registration
Statement on Form S-8 (File No. 333-32178) previously filed by the Registrant
on March 10, 2000, which registers 844,573 shares of Common Stock, the
Registration Statement on Form S-8 (File No. 333-65385) previously filed by
the Registrant on October 6, 1998, which registers 655,427 shares of Common
Stock, and the Registration Statement on Form S-8 (File No. 33-25707)
previously filed by the Registrant on April 23, 1997, which registers
1,500,000 shares of Common Stock. A filing fee in the amount of $33,627.14
was previously paid with respect to such shares.
PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE.

         We incorporate by reference the documents listed below and any future
filings we will make with the SEC under Section 13(a), 13(c), 14 or 15(d) of the
Securities Exchange Act of 1934:

         --       Annual Report on Form 10-K for the year ended December 31,
                  2000, filed on April 2, 2001;

         --       the description of our common stock contained in our
                  registration statement on Form 8-A filed with the SEC on
                  September 17, 1996, including any amendments or reports filed
                  for the purpose of updating that description; and

         --       the description of the preferred stock purchase rights for our
                  Series A Junior Participating Preferred Stock contained in our
                  registration statement on Form 8-A filed with the SEC on
                  August 2, 1999, including any amendments or reports filed for
                  the purpose of updating that description.

         You may request a copy of these filings at no cost (other than exhibits
unless those exhibits are specifically incorporated by reference herein) by
writing, telephoning or e-mailing us at the following address:

                             Cubist Pharmaceuticals, Inc.
                             24 Emily Street
                             Cambridge, MA 02139
                             Attn: Thomas A. Shea
                             (617) 576-1999
                             e-mail: tshea@cubist.com

ITEM 4.  DESCRIPTION OF SECURITIES

         Not applicable.

ITEM 5.  INTERESTS OF NAMED EXPERTS OR COUNSEL

         Not applicable.

ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

         Section 145 of the Delaware General Corporation Law empowers a Delaware
corporation to indemnify its officers and directors and certain other persons to
the extent and under the circumstances set forth therein.

         The Restated Certificate of Incorporation and the Amended and Restated
By-Laws of the Company, copies of which are filed herein as Exhibits 3.1 and
3.2, provide for advancement of expenses and indemnification of officers and
directors of the Registrant and certain other persons against liabilities and
expenses incurred by any of them in certain stated proceedings and under certain
stated conditions to the fullest extent permissible under Delaware law.

         The Company intends to maintain insurance for the benefit of its
directors and officers insuring such persons against certain liabilities,
including liabilities under the securities laws.

ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED

         Not applicable.

ITEM 8.  EXHIBITS

         The following exhibits are filed as part of this Registration
Statement:

         3.1      Restated Certificate of Incorporation of the Registrant
                  (incorporated by reference to Exhibit 3 to Cubist's Quarterly
                  Report on Form 10-Q filed on August 12, 1999) (File no.
                  000-21379).

         3.2      Amended and Restated By-Laws of the Registrant, as amended to
                  date. (incorporated by reference to Exhibit 3.4, Registration
                  No. 333-6795).

         4.1      Specimen certificate for shares of Common Stock (incorporated
                  by reference to Exhibit 3.4 to Cubist's Registration Statement
                  on Form S-1) (Registration No. 333-6795).

         4.2      Rights Agreement dated as of July 21, 1999 between Cubist and
                  BankBoston, N.A. as Rights Agent (incorporated by reference to
                  Exhibit 99.1 to Cubist's Report on Form 8-K filed on July 30,
                  1999) (File no. 000-21379).

         4.3      First Amendment, dated as of March 7, 2000, to the Rights
                  Agreement, dated as of July 21, 2000 between the Company and
                  Fleet National Bank f/k/a BankBoston, N.A., as Rights Agent
                  (incorporated herein by reference to Exhibit 4.2 to the
                  Company's Registration Statement on Form 8-A/A filed on March
                  9, 2000) (File No. 000-21379).

         4.4      Form of Amended Rights Certificate (incorporated herein by
                  reference to Exhibit 4.4 to the Company's Registration
                  Statement on Form 8-A/A filed on March 9, 2000) (File No.
                  000-21379).

         5        Opinion and Consent of Bingham Dana LLP with respect to the
                  legality of the shares being registered.

         23.1     Consent of Bingham Dana LLP (included in Exhibit 5).

         23.3     Consent of KPMG LLP.

         23.2     Consent of PricewaterhouseCoopers LLP.

         24       Power of Attorney (included in signature page to Registration
                  Statement).

ITEM 9.  UNDERTAKINGS

         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 to include any
         material information with respect to the plan of distribution not

                                       2
previously disclosed in this Registration Statement or any material
         change to such information in this Registration Statement;

(2)      That, for the purpose of determining any liability under the Securities
         Act of 1933, as amended (the "SECURITIES ACT"), 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;

(4)      That, for purposes of determining any liability under the Securities
         Act, each filing of the Registrant's annual report pursuant to Section
         13(a) or 15(d) of the Exchange Act (and, where applicable, each filing
         of an employee benefit plan's annual report pursuant to Section 15(d)
         of the Exchange Act) that is incorporated by reference in the
         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; and

(5)      Insofar as indemnification for liabilities arising under the Securities
         Act 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 SEC such
         indemnification is against public policy as expressed in the Securities
         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 Securities Act and will
         be governed by the final adjudication of such issue.

                                       3
SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, as amended,
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 the City of Cambridge, Commonwealth of Massachusetts, on
this 30th day of April, 2001.

                              CUBIST PHARMACEUTICALS, INC.

                              By: /s/ Scott M. Rocklage
                                  -------------------------------------
                                  Scott M. Rocklage, Ph.D.
                                  Chairman of the Board of Directors,
                                  President and Chief Executive Officer

                                POWER OF ATTORNEY

         Each person whose signature appears below hereby appoints Scott M.
Rocklage and Thomas A. Shea and each of them severally, acting alone and without
the other, his/her true and lawful attorney-in-fact with the authority to
execute in the name of each such person, and to file with the Securities and
Exchange Commission, together with any exhibits thereto and other documents
therewith, any and all amendments (including without limitation post-effective
amendments) to this Registration Statement on Form S-8 necessary or advisable to
enable the Registrant to comply with the Securities Act of 1933, as amended, and
any rules, regulations, and requirements of the Securities and Exchange
Commission in respect thereof, which amendments may make such other changes in
the Registration Statement as the aforesaid attorney-in-fact executing the same
deems appropriate.

         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 date indicated.
SIGNATURE                                       TITLE                                     DATE
/s/ Scott M. Rocklage                    Chairman of the Board of Directors, President,        April 30, 2001
------------------------------------     Chief Executive Officer and Director
Scott M. Rocklage                        (Principal Executive Officer)

/s/ Thomas A. Shea                       Vice President and Chief Financial Officer             April 30, 2001
------------------------------------
Thomas A. Shea

/s/ Susan Bayh                           Director                                               April 30, 2001
------------------------------------
Susan Bayh

/s/ Barry M. Bloom                       Director                                               April 30, 2001
------------------------------------
Barry M. Bloom

/s/ John K. Clarke                       Director                                               April 30, 2001
------------------------------------
John K. Clarke

/s/ David Martin                         Director                                               April 30, 2001
------------------------------------
David Martin

/s/ Walter Maupay                        Director                                               April 30, 2001
------------------------------------
Walter Maupay

/s/ Paul R. Schimmel                     Director                                               April 30, 2001
------------------------------------
Paul R. Schimmel

/s/ John Zabriskie                       Director                                               April 30, 2001
------------------------------------
John Zabriskie
INDEX TO EXHIBITS

EXHIBIT
NUMBER                            DESCRIPTION

3.1      Restated Certificate of Incorporation of the Registrant (incorporated
         by reference to Exhibit 3 to Cubist's Quarterly Report on Form 10-Q
         filed on August 12, 1999) (File no. 000-21379).

3.2      Amended and Restated By-Laws of the Registrant, as amended to date.
         (incorporated by reference to Exhibit 3.4, Registration No. 333-6795).

4.1      Specimen certificate for shares of Common Stock (incorporated by
         reference to Exhibit 3.4 to Cubist's Registration Statement on Form
         S-1) (Registration No. 333-6795).

4.2      Rights Agreement dated as of July 21, 1999 between Cubist and
         BankBoston, N.A. as Rights Agent (incorporated by reference to Exhibit
         99.1 to Cubist's Report on Form 8-K filed on July 30, 1999) (File no.
         000-21379).

4.3      First Amendment, dated as of March 7, 2000, to the Rights Agreement,
         dated as of July 21, 2000 between the Company and Fleet National Bank
         f/k/a BankBoston, N.A., as Rights Agent (incorporated herein by
         reference to Exhibit 4.2 to the Company's Registration Statement on
         Form 8-A/A filed on March 9, 2000) (File No. 000-21379)

4.4      Form of Amended Rights Certificate (incorporated herein by reference to
         Exhibit 4.4 to the Company's Registration Statement on Form 8-A/A filed
         on March 9, 2000) (File No. 000-21379)

5        Opinion and Consent of Bingham Dana LLP with respect to the legality of
         the shares being registered.

23.1     Consent of Bingham Dana LLP (included in Exhibit 5).

23.2     Consent of PricewaterhouseCoopers LLP.

23.3     Consent of KPMG LLP.

24       Power of Attorney (included in signature page to Registration
         Statement).