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                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

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

                                  FORM 10-K/A

                                AMENDMENT NO. 1

                       FOR ANNUAL AND TRANSITION REPORTS
                    PURSUANT TO SECTIONS 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934

(Mark One)

[X]   ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
      SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended:  December 31, 1997

                                       OR

[ ]   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
      SECURITIES EXCHANGE ACT OF 1934

For the transition period from ___________  to ______________

                          Commission file No.: 0-28494

                        Millennium Pharmaceuticals, Inc.
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             (Exact Name of registrant as Specified in its Charter)

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

               640 Memorial Drive, Cambridge, Massachusetts 02139
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              (Address of Principal Executive Offices) (Zip Code)

Registrant's telephone number, including area code: (617) 679-7000

Securities registered pursuant to Section 12(b) of the Act: NONE

Securities registered pursuant to Section 12(g) of the Act:

                         Common Stock, $.001 par value
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                                 Title of class


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      Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days.

                        Yes   X           No
                           ------           ------

      Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. [ ]

      The aggregate market value of voting Common Stock held by non-affiliates
of the registrant was $542,397,943, based on the last reported sale price of the
Common Stock on the Nasdaq Stock Market on March 13, 1998.

      Number of shares outstanding of the registrant's class of Common
Stock as of March 13, 1998:  29,312,329.

Documents incorporated by reference:
Annual Report to Stockholders for fiscal year ended December 31, 1997 - Part II
Proxy Statement for the 1998 Annual Meeting of Stockholders - Part III 


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                                    PART IV

ITEM 14.    EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS
            ON FORM 8-K

      (a) The following documents are included as part of this Annual Report on
Form 10-K or are incorporated by reference from the Company's 1997 Annual Report
to Stockholders.

            1.    The following financial statements (and related notes) of the
                  Company are incorporated by reference from the 1997 Annual
                  Report to Stockholders.

                  Report of Independent Auditors on Financial
                  Statements                                                35*

                  Consolidated Balance Sheets at December 31, 1997 
                  and 1996                                                  36*

                  Consolidated Statements of Operations for the years 
                  ended December 31, 1997, 1996, and 1995                   37*

                  Consolidated Statements of Cash Flows for the years 
                  ended December 31, 1997, 1996, and 1995                   38*


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                  Statements of Stockholders' Equity for the years
                  ended December 31, 1997, 1996 and 1995                    39*

                  Notes to Financial Statements                             41*

                  *Refers to page number of 1997 Annual Report to Stockholders

            2.    All schedules are omitted as the information required is
                  inapplicable or the information is presented in the
                  consolidated financial statements or the related notes.

            3.    The Exhibits listed in the Exhibit Index immediately preceding
                  the Exhibits are filed as a part of this Annual Report on Form
                  10-K.

      (b) The following Current Reports on Form 8-K were filed by the Company
during the last quarter of the period covered by this report:

            1.    Current Report on Form 8-K filed with the Securities and
                  Exchange Commission on November 4, 1997.



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                                   SIGNATURES

      Pursuant to the requirements of the Section 13 or 15(d) of the Securities
Exchange Act of 1934, the Company has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized on this 2nd day of
April, 1998.

                                    MILLENNIUM PHARMACEUTICALS, INC.


                                    By:   /S/ MARK J. LEVIN
                                          ------------------------------------
                                          Mark J. Levin
                                          Chief Executive Officer



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                                 Exhibit Index

      The following exhibits are filed as part of this Annual Report on Form
10-K. 

EXHIBIT NO.                               DESCRIPTION
-----------                               -----------

    (2)3.1   Amended and Restated Certificate of Incorporation of the Company

    (2)3.2   Amended and Restated Bylaws of the Company

    (1)4.1   Specimen Certificate for shares of Common Stock, $.001 par value,
             of the Company

(8)(1)10.1   1996 Director Option Plan

   (1)10.2   Third Amended and Restated Investors' Rights Agreement, as amended,
             dated February 1, 1996 by and among the Company and the persons
             named on the signature pages thereto.

   (1)10.3   Agreement dated as of August 10, 1995 by and between the Company
             and Joshua Boger.

   (1)10.4   Agreement dated as of August 10, 1995 by and between the Company
             and Eugene Cordes.

   (1)10.5   Agreement dated as of April 21, 1993, by and between the Company
             and Raju Kucherlapati.

   (1)10.6   Letter Agreement dated November 30, 1994 by and between the Company
             and Mark J. Levin.

   (1)10.7   Letter Agreement dated April 14, 1994 by and between the Company
             and Steven H. Holtzman.

   (1)10.8   Promissory Note dated March 15, 1996 made in favor of the Company
             by Steven H. Holtzman.

   (1)10.9   Master Lease Agreement dated March 22, 1993 by and between the
             Company and Comdisco, Inc.

  (1)10.10   Loan and Security Agreement dated October 28, 1994 by and between
             the Company and MMC/GATX Partnership No. 1


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  (1)10.11   Master Equipment Lease Agreement dated July 14, 1995 by and between
             the Company and Lighthouse Capital Partners, L.P.

  (1)10.12   Loan Agreement dated February 15, 1996 by and between the Company
             and Lighthouse Capital Partners, L.P.

  (4)10.13   Form of Master Equipment Lease Financing Agreement, as amended,
             dated September 19, 1996 by and between the Company and GE Capital
             Corporation.

  (7)10.14   Amendment to Master Equipment Lease Agreement dated June 16, 1997
             by and between the Company and GE Capital Corporation.

  (1)10.15   Lease Agreement dated August 25, 1993, as amended, by and between
             the Company and the Massachusetts Institute of Technology.

  (4)10.16   Lease Agreement dated October 26, 1996 by and between the Company
             and Fort Washington Limited Partnership

  (5)10.17   Lease Agreement between the Company and Old Cambridge Realty Trust,
             Inc.

  (5)10.18   Form of Sub-Lease Agreement, dated June 28, 1996, by and between
             the Company (as successor to ChemGenics) and PerSeptive Biosystems,
             Inc.

  (6)10.19   Lease dated March 28, 1997 by and between the Company and Old
             Cambridge Property LLC

  (6)10.20   Subordination Non-Disturbance and Attornment Agreement dated March
             28, 1997 by and among LaSalle National Bank, as Trustee for Asset
             Securitization Corporation Commercial Mortgage Pass-Through
             Certificates, Series D-4, Old Cambridge Property LLC and the
             Company.

  (7)10.21   Lease dated May 15, 1997 by and between the Company and
             Massachusetts Institute of Technology.

 (11)10.22   Lease dated November 17, 1997 by and between the Company and FC
             45/75 Sidney, Inc.

 +(1)10.23   Sponsored Research Agreement dated March 25, 1994 by and between
             the Company and F. Hoffman-La Roche Ltd.

 +(1)10.24   Research and License Agreement dated October 3, 1995 by and between
             the Company and Eli Lilly and Company.


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 +(1)10.25   Research and License Agreement dated December 9, 1995 by and
             between the Company and Astra AB.

 +(1)10.26   Research and License Agreement dated April 8, 1996 by and between
             the Company and Eli Lilly and Company.

 +(3)10.27   CNS Research, Collaboration and License Agreement effective as of
             August 1, 1996 by and between American Home Products Corporation
             and the Company.

 +(3)10.28   Bioinformatics Access and License Agreement effective as of August
             1, 1996 by and between American Home Products Corporation and the
             Company.

 +(3)10.29   Transcription Profiling Technology Access and License Agreement
             effective as of August 1, 1996 by and between American Home
             Products Corporation and the Company.

 +(5)10.30   Collaborative Research Agreement, dated as of January 1, 1995, by
             and between the Company (as successor to ChemGenics) and Pfizer,
             Inc.

 +(5)10.31   License Option, License and Royalty Agreement, dated as of January
             1, 1995, by and between the Company (as successor to ChemGenics)
             and Pfizer, Inc.

 +(5)10.32   Collaborative Research and License Agreement, dated as of November
             1, 1996, by and between the Company (as successor to ChemGenics)
             and American Home Products Corporation, represented by its
             Wyeth-Ayerst Laboratories division.

 +(5)10.33   License Agreement, dated as of June 28, 1996, by and between the
             Company (as successor to ChemGenics) and PerSeptive Biosystems,
             Inc.

  (5)10.34   Master Agreement, dated as of May 7, 1996, by and between the
             Company (as successor to ChemGenics) and PerSeptive Biosystems,
             Inc.

  (5)10.35   Amendment, dated November 22, 1996, to the Master Agreement dated
             May 7, 1996 between the Company (as successor to ChemGenics) and
             PerSeptive Biosystems, Inc.

  (5)10.36   Omnibus Amendment Agreement dated December 18, 1996 between the
             Company (as successor to ChemGenics) and PerSeptive Biosystems,
             Inc.


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  (5)10.37   Consulting and Interim Services Agreement dated as of June 28,
             1996, by and between the Company (as successor to ChemGenics) and
             PerSeptive Biosystems, Inc.

  (5)10.38   Confidentiality and Non-Competition Agreement dated as of June 28,
             1996, by and between the Company (as successor to ChemGenics) and
             PerSeptive Biosystems, Inc.

  (5)10.39   Amendment, Consent and Waiver dated January 18, 1997 by and among
             the Company, ChemGenics and American Home Products Corporation
             acting through its Wyeth-Ayerst Division ("Wyeth-Ayerst").

  (5)10.40   Letter Agreement dated January 18, 1997 by and among the Company,
             ChemGenics and Pfizer, Inc.

  (5)10.41   Letter Agreement dated January 18, 1997 by and among the Company,
             ChemGenics and PerSeptive Biosystems, Inc.

  (5)10.42   Amendment to Collaborative Research and License Agreement dated
             March 20, 1997 by and among the Company, ChemGenics and Wyeth-
             Ayerst.

 +(7)10.43   Sponsored Research Agreement by and among Whitehead Institute for
             Biomedical Research, Affymetrix, Inc., Bristol-Myers Squibb Company
             and the Company dated April 28, 1997.

 +(7)10.44   Consortium Member Agreement by and among Affymetrix, Inc., Bristol-
             Myers Squibb Company and the Company dated April 28, 1997.

 +(7)10.45   Collaboration Agreement by and among the Company, Millennium
             BioTherapeutics, Inc. ("MBIO") and Eli Lilly and Company dated as
             of May 28, 1997.

 +(7)10.46   Technology Transfer and License Agreement by and between the
             Company and MBIO dated as of May 28, 1997.

 +(7)10.47   Rights Exchange Agreement by and between the Company and MBIO dated
             as of May 28, 1997.

 +(9)10.48   Agreement dated October 27, 1997 by and among the Company, Monsanto
             Company and Cereon Genomics Inc. (formerly Monsanto Agricultural
             Genomics II LLC).


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(10)10.49    Agreement and Plan of Merger dated January 20, 1997 by and among
             the Company, CPI Acquisition Corp. and ChemGenics Pharmaceuticals,
             Inc.

(11)13       1997 Annual Report to Stockholders (which shall be deemed filed 
             only with respect to those portions specifically incorporated by
             reference herein).

(11)21       Subsidiaries of the Company.
 
    23.1     Consent of Ernst & Young LLP, Independent Auditors.

(11)27.1     Financial Data Schedule for year ended December 31, 1997.

(11)27.2     Restated Financial Data Schedule for year ended December 31, 1996.

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

(1)   Incorporated herein by reference to the Company's Registration Statement
      on Form S-1, as amended (File No. 333-2490).

(2)   Incorporated herein by reference to the Company's 10-Q for the quarter
      ending March 31, 1996.

(3)   Incorporated herein by reference to the Company's 10-Q for the quarter
      ending June 30, 1996.

(4)   Incorporated herein by reference to the Company's 10-Q for the quarter
      ending September 30, 1996.

(5)   Incorporated herein by reference to the Company's 10-K for the fiscal year
      ending December 31, 1996.

(6)   Incorporated herein by reference to the Company's 10-Q for the quarter
      ending March 31, 1997.

(7)   Incorporated herein by reference to the Company's 10-Q for the quarter
      ending June 30, 1997.

(8)   Management contract or compensatory plan or arrangement filed as an
      exhibit to this Form pursuant to Items 14(a) and 14(c) of Form 10-K.

(9)   Incorporated hereby by reference to the Company's Amendment No. 1 to
      Current Report on Form 8-K, filed with the SEC on January 30, 1998.

(10)  Incorporated herein by reference to the Company's Current Report on Form
      8-K, filed with the SEC on February 20, 1997.

(11)  Previously filed.
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+     Confidential treatment requested as to certain portions.


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