<PAGE>   1


     As filed with the Securities and Exchange Commission on August 3, 1999.
                                                   Registration No. 333-_____

- --------------------------------------------------------------------------------
          S E C U R I T I E S A N D E X C H A N G E C O M M I S S I O N
                             Washington, D.C. 20549
                                    FORM S-8
                          REGISTRATION STATEMENT UNDER
                           THE SECURITIES ACT OF 1933

                        MILLENNIUM PHARMACEUTICALS, INC.
             ------------------------------------------------------
             (Exact name of Registrant as Specified in its Charter)

            Delaware                                              04-3177038
- -------------------------------                              -------------------
(State or Other Jurisdiction of                               (I.R.S. Employer
 Incorporation or Organization)                              Identification No.)

                75 Sidney Street, Cambridge, Massachusetts 02139
               ---------------------------------------------------
               (Address of Principal Executive Offices) (Zip Code)

                        1996 EMPLOYEE STOCK PURCHASE PLAN
                        ---------------------------------
                            (Full title of the Plan)

                               John B. Douglas III
                                 General Counsel
                        Millennium Pharmaceuticals, Inc.
                75 Sidney Street, Cambridge, Massachusetts 02139
                         Cambridge, Massachusetts 02139
                     ---------------------------------------
                     (Name and Address of Agent for Service)

                                 (617) 679-7000
          -------------------------------------------------------------
          (Telephone Number, Including Area Code, of Agent For Service)

                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
================================================================================================
    Title of                               Proposed              Proposed
   Securities              Amount           Maximum               Maximum            Amount of
     to be                  to be        Offering Price          Aggregate         Registration
   Registered            Registered       Per Share (1)      Offering Price (1)         Fee
   ----------            ----------      --------------      ------------------    ------------

<S>                    <C>                   <C>                 <C>                  <C>
Common Stock,          300,000 shares        $54.75              $16,425,000          $4,567
$.001 par value
per share
- ------------------------------------------------------------------------------------------------
</TABLE>

- ------------------------
(1) Estimated solely for purposes of calculating the registration fee pursuant
to Rules 457(c) and 457(h) under the Securities Act of 1933, as amended, and
based upon the average of the high and low prices of the Common Stock on the
Nasdaq National Market on July 28, 1999.




<PAGE>   2





                     STATEMENT OF INCORPORATION BY REFERENCE


         This Registration Statement on Form S-8 incorporates by reference the
Registration Statement on Form S-8, File No. 333-15357, filed by the Registrant
on November 1, 1996, relating to the 1996 Employee Stock Purchase Plan of
Millennium Pharmaceuticals, Inc.





                                       -2-


<PAGE>   3






                                   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 the City of Cambridge, Commonwealth of Massachusetts, on this 3rd
day of August, 1999.


                                    MILLENNIUM PHARMACEUTICALS, INC.


                                    By: /s/ Mark J. Levin
                                        ----------------------------------------
                                        Mark J. Levin
                                        Chairman of the Board and
                                        Chief Executive Officer


                                POWER OF ATTORNEY


         We, the undersigned officers and directors of Millennium
Pharmaceuticals, Inc., hereby severally constitute Mark J. Levin, Kevin P. Starr
and John B. Douglas III, and each of them singly, our true and lawful attorneys
with full power to any of them, and to each of them singly, to sign for us and
in our names in the capacities indicated below, the Registration Statement on
Form S-8 filed herewith and any and all post-effective amendments to said
Registration Statement and generally to do all such things in our name and
behalf in our capacities as officers and directors to enable Millennium
Pharmaceuticals, Inc. to comply with the provisions of the Securities Act and
all requirements of the Securities and Exchange Commission, hereby ratifying and
confirming our signatures as they may be signed by our said attorneys, or any of
them, to said Registration Statement and all amendments thereto.



                                       -3-


<PAGE>   4



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

Signatures                       Capacity                         Date
- ----------                       --------                         ----

/s/ Mark J. Levin                Chairman of the Board            August 3, 1999
- ------------------------------   and Chief Executive Officer
Mark J. Levin                    (Principal Executive Officer)

/s/ Kevin P. Starr               Chief Financial Officer          July 28, 1999
- ------------------------------   (Principal Financial and
Kevin P. Starr                   Accounting Officer)

/s/ Joshua Boger                 Director                         August 3, 1999
- ------------------------------
Joshua Boger, Ph.D.

/s/ Eugene Cordes                Director                         August 3, 1999
- ------------------------------
Eugene Cordes, Ph.D.

/s/ A. Grant Heidrich            Director                         August 3, 1999
- ------------------------------
A. Grant Heidrich, III

/s/ William W. Helman            Director                         August 3, 1999
- ------------------------------
William W. Helman

/s/ Raju S. Kucherlapati         Director                         August 3, 1999
- ------------------------------
Raju S. Kucherlapati, Ph.D.

/s/ Eric S. Lander               Director                         August 3, 1999
- ------------------------------
Eric S. Lander, Ph.D.




                                       -4-


<PAGE>   5



                                  EXHIBIT INDEX

Exhibit
Number            Description
- -------           -----------

 5                Opinion of Hale and Dorr LLP.

 23.1             Consent of Ernst & Young LLP.

 23.2             Consent of Hale and Dorr LLP (included in Exhibit 5).

 24               Power of Attorney (included in the signature pages of this
                  Registration Statement).




                                       -5-
[{"type": "S-8", "sequence": "1", "description": "MILLENNIUM PHARMACEUTICALS, INC.", "secsgml_size_bytes": 7615}]
{"company-data": {"conformed-name": "MILLENNIUM PHARMACEUTICALS INC", "cik": "0001002637", "assigned-sic": "2834", "irs-number": "043177038", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "file-number": "333-84381", "film-number": "99677040"}, "business-address": {"street1": "75 SIDNEY STREET", "city": "CAMBRIDGE", "state": "MA", "zip": "02139", "phone": "6176797000"}, "mail-address": {"street1": "640 MEMORIAL DR", "city": "CAMBRIDGE", "state": "MA", "zip": "02139"}}
1

     As filed with the Securities and Exchange Commission on August 3, 1999.
                                                   Registration No. 333-_____

- --------------------------------------------------------------------------------
          S E C U R I T I E S A N D E X C H A N G E C O M M I S S I O N
                             Washington, D.C. 20549
                                    FORM S-8
                          REGISTRATION STATEMENT UNDER
                           THE SECURITIES ACT OF 1933

                        MILLENNIUM PHARMACEUTICALS, INC.
             ------------------------------------------------------
             (Exact name of Registrant as Specified in its Charter)

            Delaware                                              04-3177038
- -------------------------------                              -------------------
(State or Other Jurisdiction of                               (I.R.S. Employer
 Incorporation or Organization)                              Identification No.)

                75 Sidney Street, Cambridge, Massachusetts 02139
               ---------------------------------------------------
               (Address of Principal Executive Offices) (Zip Code)

                        1996 EMPLOYEE STOCK PURCHASE PLAN
                        ---------------------------------
                            (Full title of the Plan)

                               John B. Douglas III
                                 General Counsel
                        Millennium Pharmaceuticals, Inc.
                75 Sidney Street, Cambridge, Massachusetts 02139
                         Cambridge, Massachusetts 02139
                     ---------------------------------------
                     (Name and Address of Agent for Service)

                                 (617) 679-7000
          -------------------------------------------------------------
          (Telephone Number, Including Area Code, of Agent For Service)

                         CALCULATION OF REGISTRATION FEE
================================================================================================
    Title of                               Proposed              Proposed
   Securities              Amount           Maximum               Maximum            Amount of
     to be                  to be        Offering Price          Aggregate         Registration
   Registered            Registered       Per Share (1)      Offering Price (1)         Fee
   ----------            ----------      --------------      ------------------    ------------
Common Stock,          300,000 shares        $54.75              $16,425,000          $4,567
$.001 par value
per share
- ------------------------------------------------------------------------------------------------
- ------------------------
(1) Estimated solely for purposes of calculating the registration fee pursuant
to Rules 457(c) and 457(h) under the Securities Act of 1933, as amended, and
based upon the average of the high and low prices of the Common Stock on the
Nasdaq National Market on July 28, 1999.
2

                     STATEMENT OF INCORPORATION BY REFERENCE

         This Registration Statement on Form S-8 incorporates by reference the
Registration Statement on Form S-8, File No. 333-15357, filed by the Registrant
on November 1, 1996, relating to the 1996 Employee Stock Purchase Plan of
Millennium Pharmaceuticals, Inc.

                                       -2-
3

                                   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 the City of Cambridge, Commonwealth of Massachusetts, on this 3rd
day of August, 1999.

                                    MILLENNIUM PHARMACEUTICALS, INC.

                                    By: /s/ Mark J. Levin
                                        ----------------------------------------
                                        Mark J. Levin
                                        Chairman of the Board and
                                        Chief Executive Officer

                                POWER OF ATTORNEY

         We, the undersigned officers and directors of Millennium
Pharmaceuticals, Inc., hereby severally constitute Mark J. Levin, Kevin P. Starr
and John B. Douglas III, and each of them singly, our true and lawful attorneys
with full power to any of them, and to each of them singly, to sign for us and
in our names in the capacities indicated below, the Registration Statement on
Form S-8 filed herewith and any and all post-effective amendments to said
Registration Statement and generally to do all such things in our name and
behalf in our capacities as officers and directors to enable Millennium
Pharmaceuticals, Inc. to comply with the provisions of the Securities Act and
all requirements of the Securities and Exchange Commission, hereby ratifying and
confirming our signatures as they may be signed by our said attorneys, or any of
them, to said Registration Statement and all amendments thereto.

                                       -3-
4

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

Signatures                       Capacity                         Date
- ----------                       --------                         ----

/s/ Mark J. Levin                Chairman of the Board            August 3, 1999
- ------------------------------   and Chief Executive Officer
Mark J. Levin                    (Principal Executive Officer)

/s/ Kevin P. Starr               Chief Financial Officer          July 28, 1999
- ------------------------------   (Principal Financial and
Kevin P. Starr                   Accounting Officer)

/s/ Joshua Boger                 Director                         August 3, 1999
- ------------------------------
Joshua Boger, Ph.D.

/s/ Eugene Cordes                Director                         August 3, 1999
- ------------------------------
Eugene Cordes, Ph.D.

/s/ A. Grant Heidrich            Director                         August 3, 1999
- ------------------------------
A. Grant Heidrich, III

/s/ William W. Helman            Director                         August 3, 1999
- ------------------------------
William W. Helman

/s/ Raju S. Kucherlapati         Director                         August 3, 1999
- ------------------------------
Raju S. Kucherlapati, Ph.D.

/s/ Eric S. Lander               Director                         August 3, 1999
- ------------------------------
Eric S. Lander, Ph.D.

                                       -4-
5

                                  EXHIBIT INDEX

Exhibit
Number            Description
- -------           -----------

 5                Opinion of Hale and Dorr LLP.

 23.1             Consent of Ernst & Young LLP.

 23.2             Consent of Hale and Dorr LLP (included in Exhibit 5).

 24               Power of Attorney (included in the signature pages of this
                  Registration Statement).

                                       -5-