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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, 2003

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 |_|

Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act).
Yes |X| No |_|

Number of shares of the registrant's Common Stock, $0.001 par value, outstanding on November 10, 2003: 301,289,794


MILLENNIUM PHARMACEUTICALS, INC.

FORM 10-Q

FOR THE QUARTER ENDED SEPTEMBER 30, 2003

TABLE OF CONTENTS

    Page

 
PART I FINANCIAL INFORMATION    
       
Item 1. Condensed Consolidated Financial Statements    
       
  Condensed Consolidated Balance Sheets as of
September 30, 2003 and December 31, 2002
3      
       
  Condensed Consolidated Statements of Operations for the
three and nine months ended September 30, 2003 and 2002
4      
       
  Condensed Consolidated Statements of Cash Flows for the
nine months ended September 30, 2003 and 2002
5      
       
  Notes to Condensed Consolidated Financial Statements 6      
       
Item 2. Management's Discussion and Analysis of Financial
Condition and Results of Operations
15      
       
  Risk Factors That May Affect Results 29      
       
Item 3. Quantitative and Qualitative Disclosures About Market Risk 40      
       
Item 4. Controls and Procedures 41      
       
PART II OTHER INFORMATION    
       
Item 6. Exhibits and Reports on Form 8-K 42      
       
  Signatures 43      
       
  Exhibit Index 44      
       

The following Millennium trademarks are used in this Quarterly Report on Form 10-Q: Millennium®, the Millennium “M” logo and design (registered), Millennium Pharmaceuticals™, VELCADE™ (bortezomib) for Injection, and INTEGRILIN® (eptifibatide) Injection. All are covered by registrations or pending applications for registration in the U.S. Patent and Trademark Office and many other countries. CAMPATH® is a registered trademark of ILEX Pharmaceuticals, L.P., ReoPro® is a trademark of Eli Lilly and Company, Aggrastat® is a trademark of Merck & Co., Inc. and Thalomid® (thalidomide) is a registered trademark of Celgene Corporation. 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, 2003
  December 31, 2002
 
  (unaudited)      
(in thousands, except per share amounts)    
Assets    
Current assets:                
Cash and cash equivalents     $ 75,719   $ 1,332,391  
Marketable securities       844,017     426,672  
Accounts receivable       29,170      
Due from strategic alliance partners       104,387     44,869  
Inventory       114,490     105,346  
Prepaid expenses and other current assets       22,763     29,463  
     

 

 
Total current assets       1,190,546     1,938,741  
Property and equipment, net       247,133     310,325  
Restricted cash       21,244     31,056  
Other assets       20,386     33,168  
Goodwill       1,201,246     1,200,510  
Developed technology, net       380,625     405,721  
Intangible assets, net       60,583     78,086  
     

 

 
Total assets     $ 3,121,763   $ 3,997,607  
     

 

 
                 
Liabilities and Stockholders' Equity                
Current liabilities:                
Accounts payable     $ 19,972   $ 34,216  
Accrued expenses       150,391     181,318  
Current portion of deferred revenue       90,871     118,008  
Current portion of capital lease obligations       15,319     16,045  
Current portion of long term debt           599,960  
     

 

 
Total current liabilities       276,553     949,547  
Deferred revenue, net of current portion       13,427     1,704  
Capital lease obligations, net of current portion       91,019     61,338  
Long term debt, net of current portion       105,461     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:
300,154 shares at September 30, 2003 and 291,094 shares at
December 31, 2002 issued and outstanding
      300     291  
Additional paid-in capital       4,494,992     4,432,040  
Deferred compensation       (613 )   (1,952 )
Accumulated other comprehensive income       10,712     4,119  
Accumulated deficit       (1,870,088 )   (1,532,805 )
     

 

 
Total stockholders' equity       2,635,303     2,901,693  
     

 

 
Total liabilities and stockholders' equity     $ 3,121,763   $ 3,997,607  
     

 

 

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,
 
  2003
  2002
  2003
  2002
 
(in thousands, except per share amounts)  
                                 
Revenues:                                
    Net product sales     $ 23,046   $       $ 30,915   $  
    Co-promotion revenue       47,855     45,035         151,887     112,104  
    Revenue under strategic alliances       73,930     50,720         165,466     144,104  
     

 

     

 

 
        Total revenues       144,831     95,755         348,268     256,208  
     

 

     

 

 
Costs and expenses:                                
    Cost of goods sold       17,763     14,309         49,024     33,891  
    Research and development       119,741     140,522         377,126     364,264  
    Selling, general and administrative       43,018     41,844         122,223     125,084  
    Restructuring charges       52,736             146,241      
    Acquired in-process research and development                       242,000  
    Amortization of intangibles       9,676     9,810         29,028     25,107  
     

 

     

 

 
        Total costs and expenses       242,934     206,485         723,642     790,346  
     

 

     

 

 
Loss from operations       (98,103 )   (110,730 )       (375,374 )   (534,138 )
                                 
Other income (expense):                                
    Investment income, net       8,493     22,234         26,797     65,283  
    Interest expense       (2,675 )   (10,383 )       (18,210 )   (27,624 )
    Gain on sale of equity interest in joint venture                   40,000     40,000  
    Debt financing charge                   (10,496 )   (54,000 )
     

 

     

 

 
Net loss     $ (92,285 ) $ (98,879 )     $ (337,283 ) $ (510,479 )
     

 

     

 

 
Amounts per common share:                                
Net loss per share, basic and diluted     $ (0.31 ) $ (0.35 )     $ (1.14 ) $ (1.86 )
     

 

     

 

 
Weighted average shares, basic and diluted       299,030     285,091         296,424     274,013  
     

 

     

 

 

See notes to condensed consolidated financial statements.

4


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

  Nine Months Ended September 30,
 
  2003
  2002
 
(in thousands)    
                 
Cash Flows from Operating Activities:                
Net loss     $ (337,283 ) $ (510,479 )
Adjustments to reconcile net loss to cash                
used in operating activities:                
Acquired in-process research and development           242,000  
Depreciation and amortization       78,809     61,408  
Restructuring charges       79,202    
Amortization of deferred financing costs       12,083   2,688  
(Gain) loss on marketable securities, net       (2,983 )   4,549  
Stock compensation expense       7,035     6,887  
Changes in operating assets and liabilities:                
  Accounts receivable       (29,170 )    
  Due from strategic alliance partners       (69,518 )   (45,493 )
  Prepaid expenses and other current assets       (3,467 )   379  
  Restricted cash and other assets       25,339     (5,957 )
  Accounts payable and accrued expenses       46,597     15,546  
  Deferred revenue       (15,414 )   (40,648 )
     

 

 
Net cash used in operating activities       (208,770 )   (269,120 )
     

 

 
                 
Cash Flows from Investing Activities:                
Investments in marketable securities       (977,860 )   (845,467 )
Proceeds from sales and maturities of marketable securities       565,853     850,382  
Other investing activity       (4,111 )   (235 )
Purchase of property and equipment and other long term assets       (45,096 )   (101,225 )
Net cash acquired in COR Therapeutics, Inc. acquisition           308,522  
     

 

 
Net cash (used in) provided by investing activities       (461,214 )   211,977  
     

 

 
                 
Cash Flows from Financing Activities:                
Proceeds from sales of common stock