<PAGE>   1


                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM 10-Q

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

     For the quarterly period ended June 30, 1998

     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 NUMBER 0-28494

                        MILLENNIUM PHARMACEUTICALS, INC.
             (Exact name of registrant as specified in its charter)


            DELAWARE                                     04-3177038
(State or other jurisdiction of             (I.R.S. Employer Identification No.)
 incorporation or organization)


                      238 MAIN STREET, CAMBRIDGE, MA 02142
          (Address of principal executive offices, including zip code)

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


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 [ ]

Number of shares of Common Stock, $.001 par value per share, outstanding as of
August 6, 1998 was 29,547,516.




                                       
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                        MILLENNIUM PHARMACEUTICALS, INC.
                               REPORT ON FORM 10-Q
                  FOR THE QUARTERLY PERIOD ENDED JUNE 30, 1998


                                TABLE OF CONTENTS


                                                                           PAGE
                                                                           ----
PART I - FINANCIAL INFORMATION

ITEM 1.   FINANCIAL STATEMENTS (unaudited)
            Condensed Consolidated Balance Sheets                            
               June 30, 1998 and December 31, 1997                           3

            Condensed Consolidated Statements of Operations 
               and Comprehensive Loss for the three and six 
               months ended June 30, 1998 and 1997                           4

            Condensed Consolidated Statements of Cash Flows
               for the six months ended June 30, 1998 and 1997               5

            Notes to Condensed Consolidated Financial Statements             6

ITEM 2.   MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
          CONDITION AND RESULTS OF OPERATIONS                                7

PART II - OTHER INFORMATION                                                 10

ITEM 4.   SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS               10

ITEM 6.   EXHIBITS AND REPORTS ON FORM 8-K                                  11

SIGNATURES                                                                  12
EXHIBIT INDEX                                                               13



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                        Millennium Pharmaceuticals, Inc.
                      Condensed Consolidated Balance Sheets

<TABLE>
<CAPTION>


                                                                      JUNE 30,      DECEMBER 31,
(in thousands, except par value and shares)                             1998           1997
                                                                      -------       -----------
                                                                    (Unaudited)       (Note)
<S>                                                                  <C>            <C>

ASSETS
Current assets:
Cash and cash equivalents                                            $  34,078       $  69,236
Marketable securities                                                   40,472          27,321
Due from strategic partners                                             10,226             778
Prepaid expenses and other current assets                                3,139           4,595
                                                                     ---------       ---------
Total current assets                                                    87,915         101,930

Property and equipment, net                                             32,953          29,030
Restricted cash and other assets                                        11,737           5,140
Intangible assets, net                                                   7,062           8,413
                                                                     ---------       ---------

                                                                     $ 139,667       $ 144,513
                                                                     =========       =========

LIABILITIES AND STOCKHOLDERS' EQUITY 
Current liabilities:
Accounts payable                                                     $   5,647       $   3,165
Accrued expenses                                                         5,203           4,294
Deferred revenue                                                         2,507           3,053
Current portion of capital lease obligations                             7,505           5,847
                                                                     ---------       ---------
Total current liabilities                                               20,862          16,359

Capital lease obligations, net of current portion                       20,330          19,809
Minority interest                                                       10,588          16,590
Commitments and contingencies

Stockholders' equity:
Preferred Stock, $0.001 par value; 5,000,000 shares authorized;
 none issued                                                                --              --
Common Stock, $0.001 par value: 100,000,000 shares authorized;
 29,530,230 shares in 1998 and 29,169,398 shares in 1997 issued
 and outstanding                                                            30              29

Additional paid-in capital                                             195,372         193,254
Deferred compensation                                                   (1,373)         (1,992)
Notes receivable from officers                                            (126)           (166)
Unrealized gain (loss) on marketable securities                            (23)             (4)
Accumulated deficit                                                   (105,993)        (99,366)
                                                                     ---------       ---------
Total stockholders' equity                                              87,887          91,755
                                                                     ---------       ---------

Total liabilities and stockholders' equity                           $ 139,667       $ 144,513
                                                                     =========       =========

</TABLE>



Note: The balance sheet at December 31, 1997 has been derived from the audited
financial statements at that date but does not include all of the information
and footnotes required by generally accepted accounting principles for complete
financial statements.

See notes to condensed consolidated financial statements.





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                        Millennium Pharmaceuticals, Inc.
                Condensed Consolidated Statements of Operations
                       and Comprehensive Loss (Unaudited)


<TABLE>
<CAPTION>
                                                           THREE MONTHS ENDED                     SIX MONTHS ENDED
                                                                JUNE 30,                              JUNE 30,
                                                        1998               1997              1998              1997
                                                      ----------        ----------        ----------        ----------
<S>                                                  <C>               <C>               <C>               <C>        
(in thousands, except per share and share data)
----------------------------------------------

Revenue under strategic alliances                    $    28,236       $    13,372       $    49,279       $    24,328

Costs and expenses:
   Research and development                               28,036            18,333            50,465            29,932
   General and administrative                              5,927             4,514            11,838             7,863
   Acquired in-process research and development
                                                              --                --                --            83,800
   Amortization of intangible assets                         676               675             1,351             1,046
                                                     -----------       -----------       -----------       -----------
                                                          34,639            23,522            63,654           122,641
                                                     -----------       -----------       -----------       -----------
Loss from operations                                      (6,403)          (10,150)          (14,375)          (98,313)

Interest income                                            1,339               976             2,786             2,053
Interest expense                                            (479)             (303)           (1,124)             (636)
Minority interest                                          3,342                --             6,086                --
                                                     -----------       -----------       -----------       -----------

Net Loss                                             $    (2,201)      $    (9,477)      $    (6,627)      $   (96,896)

Unrealized gain (loss) on marketable securities               19                84               (19)               (4)
                                                     -----------       -----------       -----------       -----------

Comprehensive loss                                        (2,182)           (9,393)           (6,646)          (96,900)    
                                                     ===========       ===========       ===========       ===========

Basic and diluted net loss per share                 $     (0.07)      $     (0.33)      $     (0.23)      $     (3.50)

Shares used in computing basic and diluted net
   loss per share                                     29,500,860        28,764,467        29,396,532        27,663,696
                                                     ===========       ===========       ===========       ===========

</TABLE>



See notes to condensed consolidated financial statements.


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<PAGE>   5
                        Millennium Pharmaceuticals, Inc.
           Condensed Consolidated Statements of Cash Flows (Unaudited)


<TABLE>
<CAPTION>

SIX MONTHS ENDED JUNE 30,                                  1998           1997
(in thousands)                                           --------       --------
<S>                                                      <C>            <C>      

CASH USED IN OPERATIONS                                  $(17,906)      $ (5,874)


INVESTING ACTIVITIES
Purchase of property and equipment                         (3,004)        (4,842)
Sale of marketable securities                              35,785         37,805
Purchase of marketable securities                         (48,936)       (23,487)
                                                         --------       -------- 
Net cash (used in) provided by investing activities       (16,155)         9,476

FINANCING ACTIVITIES
Acquisition of ChemGenics, net of cash acquired                --          7,087
Net proceeds from employee stock purchases                  2,134            910
Repurchase of Common Stock                                    (15)           (86)
Payments of long-term debt                                     --           (800)
Payments of capital lease obligations                      (3,216)        (2,210)
                                                         --------       -------- 
Net cash (used in) provided by financing activities        (1,097)         4,901
                                                         --------       -------- 

(Decrease) increase in cash and cash equivalents          (35,158)         8,503
Cash and cash equivalents at beginning of period           69,236         10,088
                                                         --------       -------- 

Cash and cash equivalents at end of period               $ 34,078       $ 18,591
                                                         ========       ========

NON-CASH INVESTING AND FINANCING ACTIVITIES:
Equipment acquired under capital leases                  $  5,395       $  6,202
                                                         ========       ========


</TABLE>


See notes to condensed consolidated financial statements.





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                        MILLENNIUM PHARMACEUTICALS, INC.

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

                                  JUNE 30, 1998
                                   (unaudited)

         1 - BASIS OF PRESENTATION

         The accompanying condensed consolidated financial statements have been
prepared in accordance with generally accepted accounting principles for interim
financial information and with the instructions to Form 10-Q and Article 10 of
Regulation S-X. Accordingly, they do not include all of the information and
footnotes required by generally accepted accounting principles for complete
financial statements. In the opinion of management, all adjustments (consisting
of normal recurring accruals) considered necessary for a fair presentation have
been included. Interim results for the six-month period ended June 30, 1998 are
not necessarily indicative of the results that may be expected for the year
ended December 31, 1998. For further information, refer to the financial
statements and footnotes thereto included in the Company's Annual Report on 10-K
for the fiscal year ended December 31, 1997 which was filed with the Securities
Exchange Commission on March 26, 1998.

         As of January 1, 1998, the Company adopted Statement 130, Reporting
Comprehensive Income. Statement 130 establishes new rules for the reporting and
display of comprehensive income and its components; however, the adoption of
this Statement had no impact on the Company's net loss or shareholders' equity.
Statement 130 requires unrealized gains or losses on the Company's
available-for-sale securities, which prior to adoption were reported separately
in shareholders' equity, to be included in other comprehensive income. Prior 
year financial statements have been reclassified to conform to the requirements
of Statement 130.




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<PAGE>   7

ITEM 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
         OF OPERATIONS.

         This Report on Form 10-Q contains forward-looking statements. For this
purpose, any statements contained herein that are not statements of historical
fact may be deemed to be forward-looking statements. Without limiting the
foregoing, the words "believes," "anticipates," "plans," "expects," "intends,"
and similar expressions are intended to identify forward-looking statements.
There are a number of important factors that could cause the Company's actual
results to differ materially from those indicated by such forward-looking
statements. These factors are set forth under the caption "Factors That May
Affect Results" in the Company's Annual Report on Form 10-K for the year ended
December 31, 1997, which "Factors That May Affect Results" discussion is
expressly incorporated by reference herein.

OVERVIEW

         Millennium Pharmaceuticals, Inc. ("Millennium" or the "Company"), was
incorporated in January 1993 and is applying a comprehensive platform of
genomics and related technologies to pursue multiple opportunities in the
discovery and development of life-science-based products and services. Most of
the Company's activities currently are directed at the field of human
healthcare. As used herein, the terms "the Company" and "Millennium" include
the Company's subsidiaries where appropriate in the context.

RESULTS OF OPERATIONS

         QUARTERS ENDED JUNE 30, 1998 AND JUNE 30, 1997

         Revenue under strategic alliances increased to $28.2 million for the
three months ended June 30, 1998 (the "1998 Quarterly Period") from $13.4
million for the three months ended June 30, 1997 (the "1997 Quarterly Period").
The increase in revenue in the 1998 Quarterly Period is due primarily to
revenue from research funding and payments for technology transfer under the
Company's alliance with Monsanto Company (the "Monsanto alliance"). The
Monsanto alliance was entered into in October 1997 and, therefore, was not in
place in the 1997 Quarterly Period.

         Research and development expenses increased to $28.0 million for the
1998 Quarterly Period from $18.3 million for the 1997 Quarterly Period. The
increase was attributable primarily to increased personnel expenses as the
Company hired additional research and development personnel, increased purchases
of laboratory supplies, and increased equipment depreciation and facilities
expenses in connection with the expansion of the Company's research efforts.

         General and administrative expenses increased to $5.9 million for the
1998 Quarterly Period from $4.5 million for the 1997 Quarterly Period. The
increase was attributable primarily to increased personnel expenses as the
Company hired additional management, business 


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<PAGE>   8
development and administrative personnel, and to professional fees in
connection with the further expansion of the Company's operations.

         The Company's total operating expenses increased to $34.6 million for
the 1998 Quarterly Period from $23.5 million for the 1997 Quarterly Period.

         Interest income was $1.3 million for the 1998 Quarterly Period and $1.0
million for the 1997 Quarterly Period. The increase resulted from an increase in
the Company's average balance of cash, cash equivalents and marketable
securities. Interest expense increased to $.5 million for the 1998 Quarterly
Period from $.3 million for the 1997 Quarterly Period due to increased capital
lease obligations.

         Minority interest represents the minority shareholder interest of Eli
Lilly and Company ("Lilly") in the net loss for the 1998 Quarterly Period of the
Company's majority-owned subsidiary, Millennium BioTherapeutics, Inc. ("MBio").

         SIX MONTHS ENDED JUNE 30, 1998 AND JUNE 30, 1997

         Revenue under strategic alliances increased to $49.3 million for the
six months ended June 30, 1998 (the "1998 Six Month Period") from $24.3 million
for the six months ended June 30, 1997 (the "1997 Six Month Period"). The
increase is due primarily to revenue from research funding and the achievement
of mutually agreed upon technology transfer objectives relating to the Monsanto
alliance which was not in place during the 1997 Six Month Period. In addition,
revenue relating to MBio's alliance with Lilly during the 1998 Six Month Period
increased compared to the 1997 Six Month Period. The increase in revenues under
the alliance with Lilly is primarily due to the fact that the research program
with Lilly commenced late in the 1997 Six Month Period. 

         Research and development expenses increased to $50.5 million for the
1998 Six Month Period from $29.9 million for the 1997 Six Month Period. The
increase was attributable primarily to increased personnel expenses as the
Company hired additional research and development personnel, increased purchases
of laboratory supplies, and increased equipment depreciation and facilities
expenses in connection with the expansion of the Company's research efforts.

         General and administrative expenses increased to $11.8 million for the
1998 Six Month Period from $7.9 million for the 1997 Six Month Period. The
increase was attributable primarily to increased personnel expenses as the
Company hired additional management, business development and administrative
personnel, and to professional fees in connection with the further expansion of
the Company's operations.

         The Company's total operating expenses decreased to $63.7 million for
the 1998 Six Month Period from $122.6 million for the 1997 Six Month Period. The
decrease is primarily attributable to a one-time charge of $83.8 million in the
1997 Six Month Period for acquired in-process research and development
associated with the Company's acquisition of ChemGenics Pharmaceuticals, Inc.



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<PAGE>   9
         Interest income was $2.8 million for the 1998 Six Month Period compared
to $2.1 million for the 1997 Six Month Period. The increase resulted from an
increase in the Company's average balance of cash, cash equivalents and
marketable securities. Interest expense increased to $1.1 million for the 1998
Six Month Period from $.6 million for the 1997 Six Month Period due to increased
capital lease obligations.

         Minority interest represents the minority shareholder interest of Lilly
in the net loss for the 1998 Six Month Period of the Company's majority owned
subsidiary, MBio.

LIQUIDITY AND CAPITAL RESOURCES

         Since inception, the Company has recognized approximately $201.8
million of revenue under strategic alliances. As of June 30, 1998, the Company
had approximately $74.6 million in cash, cash equivalents and marketable
securities. This excludes $9.8 million of marketable securities classified as
restricted cash and other assets on the balance sheet which serve as collateral
for the Company's letters of credit.

         During the six months ended June 30, 1998, the Company used $17.9
million of cash in its operations, purchased $3.0 million of property and
equipment and used cash of $3.2 million to pay capital lease obligations. In
addition, during the six months ended June 30, 1998, the Company acquired
equipment under capital leases of $5.4 million.

         The Company believes that existing cash and marketable securities and
anticipated cash payments from its strategic alliances will be sufficient to
support the Company's operations for the next twelve months.

IMPACT OF YEAR 2000

         Based on a recent assessment, the Company determined that it will not
be required to modify or replace significant portions of its software so that
its computer systems will function properly with respect to dates in the year
2000 and thereafter. The Company's systems are based upon technology acquired in
the last few years. Therefore, the Company presently believes that no
significant modifications to existing software are needed based on presently
available information.




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<PAGE>   10
                          PART II - OTHER INFORMATION


ITEM 4.    SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

     The Company's 1998 Annual Meeting of Stockholders was held on June 2, 1998
(the "Annual Meeting"). At the Annual Meeting, Eugene Cordes, Raju Kucherlapati
and Eric S. Lander were elected as Class II Directors for a three year term. The
other directors whose terms of office as a director continue after the meeting
are as follows: Mark J. Levin, Joshua Boger, A. Grant Heidrich and William W.
Helman.

     The following is a summary of each matter voted at the meeting and the
number of votes cast for, against or withheld, and abstentions, as to each such
matter:

1.   To elect three Class II Directors for the ensuing three years.

     For:  22,948,522              Withheld:  15,020

2.   To ratify the selection by the Board of Directors of Ernst & Young LLP as
     the Company's independent auditors for 1998.  
   
     For:  22,943,092       Against:  10,850       Abstain:  9,600


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Item 6.   EXHIBITS AND REPORTS ON FORM 8-K.

     (a)  Exhibits

          The exhibits listed in the Exhibit Index are included in this report.

     (b)  Reports on Form 8-K

          None.






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                                   SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.


                                             MILLENNIUM PHARMACEUTICALS, INC.
                                                    (Registrant)






Date: August 12, 1998                   By:  /s/ Janet C. Bush
                                            ---------------------------------- 
                                            Janet C. Bush
                                            Vice President, Finance
                                            (Principal Financial Officer)


Date: August 12, 1998                   By: /s/ William J. Curry
                                            ----------------------------------
                                            William J. Curry
                                            Controller
                                            (Principal Accounting Officer)







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                                  EXHIBIT INDEX

         The following exhibits are filed as part of this Quarterly Report on
Form 10-Q:


Exhibit
  No.             Description
-------           -----------
  10.1            Lease dated June 12, 1998 by and between the Company and 270
                  Albany Street Realty Trust.

  10.2            Lease dated June 17, 1998 by and between the Company and
                  Transamerica Business Credit Corporation.

  27.1            Financial Data Schedule for the quarter ended June 30, 1998

  27.2            Restated Financial Data Schedule for the quarter ended
                  June 30, 1997

  99.1            Pages 44 through 58 of the Company's Annual Report of Form
                  10-K for the year ended December 31, 1997, as filed with the
                  Securities Exchange Commission (which are deemed filed except
                  to the extent that portions are not expressly incorporated by
                  reference herein).






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