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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, DC 20549


FORM 10-Q


(Mark One)

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

For the quarterly period ended September 30, 2002

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 incorporation or organization)
  (I.R.S. Employer
Identification No.)

75 Sidney Street, Cambridge, Massachusetts 02139
(Address of principal executive offices) (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 |_|

The total number of shares of the registrant's Common Stock, $0.001 par value, outstanding on November 11, 2002, was 287,785,551.


MILLENNIUM PHARMACEUTICALS, INC.

FORM 10-Q

FOR THE QUARTER ENDED SEPTEMBER 30, 2002

TABLE OF CONTENTS

    Page
 
   
 
PART I FINANCIAL INFORMATION    
       
Item 1. Condensed Consolidated Financial Statements    
       
  Condensed Consolidated Balance Sheets as of
September 30, 2002 and December 31, 2001
3      
       
  Condensed Consolidated Statements of Operations for the
three and nine months ended September 30, 2002 and 2001
4      
       
  Condensed Consolidated Statements of Cash Flows for the
nine months ended September 30, 2002 and 2001
5      
       
  Notes to Condensed Consolidated Financial Statements 6      
       
Item 2. Management's Discussion and Analysis of Financial
Condition and Results of Operations
13      
       
  Risk Factors That May Affect Results 23      
       
Item 3. Quantitative and Qualitative Disclosures about Market Risk 32      
       
Item 4. Controls and Procedures 32      
       
PART II OTHER INFORMATION    
       
Item 2. Changes in Securities and Use of Proceeds 33      
       
Item 6. Exhibits and Reports on Form 8-K 33      
       
  Signatures 34      
       
  Certifications 35      
       
  Exhibit Index 37      
       

The following Millennium trademarks are used in this Quarterly Report on Form 10-Q:  Diagnomics™, Melastatin®, Millennium®, Millennium Pharmaceuticals™, VELCADE™ (bortezomib) for Injection and INTEGRILIN® (eptifibatide) Injection. CAMPATH® is a registered trademark of ILEX Pharmaceuticals, L.P., TNKase™ and Activase® are trademarks of Genentech, Inc., ReoPro® is a trademark of Eli Lilly and Company and Aggrastat® is a trademark of Merck & Co., Inc. Other trademarks used in this Quarterly Report on Form 10-Q are the property of their respective owners.

2


PART I     FINANCIAL INFORMATION

Item 1.    Condensed Consolidated Financial Statements

Millennium Pharmaceuticals, Inc.
Condensed Consolidated Balance Sheets

  September 30, 2002
  December 31, 2001
 
  (unaudited)      
(in thousands, except per share amounts)    
Assets    
Current assets:                
Cash and cash equivalents     $ 62,815   $ 35,993  
Marketable securities       1,758,685     1,438,875  
Due from strategic alliance partners       36,892     18,360  
Inventory       105,095      
Prepaid expenses and other current assets       67,495     21,389  
     

 

 
Total current assets       2,030,982     1,514,617  
Property and equipment, net       277,437     168,600  
Restricted cash       38,942     47,308  
Other assets       30,453     13,362  
Goodwill, net       1,201,491     138,519  
Intangible assets, net       493,616     25,328  
     

 

 
Total assets     $ 4,072,921   $ 1,907,734  
     

 

 
                 
Liabilities and Stockholders' Equity                
Current liabilities:                
Accounts payable     $ 25,697   $ 25,237  
Accrued expenses       164,944     89,372  
Current portion of deferred revenue       136,935     71,018  
Current portion of capital lease obligations       16,942     17,536  
Current portion of long term debt       599,960      
     

 

 
Total current liabilities       944,478     203,163  
Deferred revenue, net of current portion       5,767     17,902  
Capital lease obligations, net of current portion       61,718     35,107  
Long term debt, net of current portion       83,325     83,325  
         
Commitments and contingencies                
         
Stockholders' equity:                
Preferred Stock, $0.001 par value; 5,000 shares authorized, none
    issued
           
Common Stock, $0.001 par value; 500,000 shares authorized:
    286,990 shares at September 30, 2002 and 224,290 shares at
    December 31, 2001 issued and outstanding
      287     224  
Additional paid-in capital       4,398,353     2,477,334  
Deferred compensation       (2,512 )   (765 )
Notes receivable from officers       (24 )   (315 )
Accumulated other comprehensive income       34,620     34,371  
Accumulated deficit       (1,453,091 )   (942,612 )
     

 

 
Total stockholders' equity       2,977,633     1,568,237  
     

 

 
Total liabilities and stockholders' equity     $ 4,072,921   $ 1,907,734  
     

 

 

See notes to condensed consolidated financial statements.

3


Millennium Pharmaceuticals, Inc.
Condensed Consolidated Statements of Operations
(unaudited)

  Three Months Ended September 30,
  Nine Months Ended September 30,
 
  2002
  2001
  2002
  2001
 
(in thousands, except per share amounts)  
                                 
Revenues:                                
    Revenue under strategic alliances     $ 50,720   $ 82,175       $ 144,104   $ 191,605  
    Copromotion revenue       45,035             112,104      
     

 

     

 

 
        Total revenues       95,755     82,175         256,208     191,605  
     

 

     

 

 
Costs and expenses:                                
    Research and development       140,522     98,840         364,264     285,945  
    Selling, general and administrative       37,391     18,315         114,691     53,948  
    Cost of copromotion revenue       18,762             44,284      
    Acquired in-process research and development                   242,000      
    Amortization of intangibles       9,810     15,714         25,107     48,010  
     

 

     

 

 
        Total costs and expenses       206,485     132,869         790,346     387,903  
     

 

     

 

 
Loss from operations       (110,730 )   (50,694 )       (534,138 )   (196,298 )
                                 
Other income (expense):                                
    Investment income       21,722     24,007         69,832     73,392  
    Realized gain on marketable securities       3,818     1,363         15,819     6,519  
    Realized loss on marketable securities       (3,306 )   (169 )       (20,368 )   (760 )
    Interest expense       (10,383 )   (2,366 )       (27,624 )   (7,020 )
    Gain on sale of equity interest in joint venture                   40,000      
    Equity in operations of joint venture           2,625             1,700  
    Debt financing charge                   (54,000 )    
    Debt conversion expenses                       (2,567 )
     

 

     

 

 
Net loss     $ (98,879 ) $ (25,234 )     $ (510,479 ) $ (125,034 )
     

 

     

 

 
Amounts per common share:                                
Net loss per share, basic and diluted     $ (0.35 ) $ (0.11 )     $ (1.86 ) $ (0.57 )
     

 

     

 

 
Weighted average shares, basic and diluted       285,091     220,069         274,013     217,766  
     

 

     

 

 

See notes to condensed consolidated financial statements.

4


Millennium Pharmaceuticals, Inc.
Condensed Consolidated Statements of Cash Flows
(unaudited)

  Nine Months Ended September 30,
 
  2002
  2001
 
(in thousands)    
                 
Cash Flows from Operating activities:                
Net loss     $ (510,479 ) $ (125,034 )
Adjustments to reconcile net loss to cash used in operating activities:                
    Acquired in-process research and development       242,000      
    Depreciation and amortization       61,408     72,938  
    (Gain) on marketable securities       (15,819 )   (6,519 )
    Loss on marketable securities       20,368     760  
    Stock compensation expense       6,887     3,214  
    Equity in operations of joint venture           (1,700 )
    Changes in operating assets and liabilities:                
        Due from strategic alliance partners       (5,493 )   (7,948 )
        Prepaid expenses and other current assets       (39,621 )   (1,194 )
        Restricted cash and other assets       (3,269 )   251  
        Accounts payable and accrued expenses       (20,652 )   9,848  
        Deferred revenue       (40,648 )   (54,065 )
     

 

 
Net cash used in operating activities       (305,318 )   (109,449 )
     

 

 
                 
Cash Flows from Investing activities:                
Investments in marketable securities       (845,467 )   (616,545 )
Proceeds from sales and maturities of marketable securities       850,382     474,992  
Investment in joint venture       (235 )   (656 )
Purchase of property and equipment and other long term assets       (65,027 )   (36,158 )
Net cash used in Cambridge Discovery Chemistry Ltd. acquisition           (1,614 )
Proceeds from the sale of Cambridge Discovery Chemistry, Inc.           946  
Net cash acquired in COR Therapeutics, Inc. acquisition       308,522