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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 June 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 August 8, 2003: 298,703,411


MILLENNIUM PHARMACEUTICALS, INC.

FORM 10-Q

FOR THE QUARTER ENDED JUNE 30, 2003

TABLE OF CONTENTS

    Page

 
PART I FINANCIAL INFORMATION    
       
Item 1. Condensed Consolidated Financial Statements    
       
  Condensed Consolidated Balance Sheets as of
June 30, 2003 and December 31, 2002
3      
       
  Condensed Consolidated Statements of Operations for the
three and six months ended June 30, 2003 and 2002
4      
       
  Condensed Consolidated Statements of Cash Flows for the
six months ended June 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 27      
       
Item 3. Quantitative and Qualitative Disclosures about Market Risk 38      
       
Item 4. Controls and Procedures 38      
       
PART II OTHER INFORMATION    
       
Item 4. Submission of Matters to a Vote of Security Holders 40      
       
Item 6. Exhibits and Reports on Form 8-K 40      
       
  Signatures 42      
       
  Exhibit Index 43      
       

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

  June 30, 2003
  December 31, 2002
 
  (unaudited)      
(in thousands, except per share amounts)    
Assets    
Current assets:                
Cash and cash equivalents     $ 43,493   $ 1,332,391  
Marketable securities       922,326     426,672  
Accounts receivable       8,031      
Due from strategic alliance partners       84,634     44,869  
Inventory       111,289     105,346  
Prepaid expenses and other current assets       70,332     29,463  
     

 

 
Total current assets       1,240,105     1,938,741  
Property and equipment, net       258,757     310,325  
Restricted cash       21,244     31,056  
Other assets       20,798     33,168  
Goodwill       1,201,214     1,200,510  
Developed technology, net       388,990     405,721  
Intangible assets, net       61,894     78,086  
     

 

 
Total assets     $ 3,193,002   $ 3,997,607  
     

 

 
                 
Liabilities and Stockholders' Equity                
Current liabilities:                
Accounts payable     $ 16,887   $ 34,216  
Accrued expenses       154,273     181,318  
Current portion of deferred revenue       115,910     118,008  
Current portion of capital lease obligations       15,660     16,045  
Current portion of long term debt           599,960  
     

 

 
Total current liabilities       302,730     949,547  
Deferred revenue, net of current portion       13,838     1,704  
Capital lease obligations, net of current portion       54,894     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:
298,198 shares at June 30, 2003 and 291,094 shares at
December 31, 2002 issued and outstanding
      298     291  
Additional paid-in capital       4,481,526     4,432,040  
Deferred compensation       (1,082 )   (1,952 )
Accumulated other comprehensive income       13,140     4,119  
Accumulated deficit       (1,777,803 )   (1,532,805 )
     

 

 
Total stockholders' equity       2,716,079     2,901,693  
     

 

 
Total liabilities and stockholders' equity     $ 3,193,002   $ 3,997,607  
     

 

 

See notes to condensed consolidated financial statements.

3


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

  Three Months Ended June 30,
  Six Months Ended June 30,
 
  2003
  2002
  2003
  2002
 
(in thousands, except per share amounts)  
                                 
Revenues:                                
    Net product sales     $ 7,869   $       $ 7,869   $  
    Co-promotion revenue       53,151     44,927         104,032     67,069  
    Revenue under strategic alliances       60,702     46,927         91,536     93,384  
     

 

     

 

 
        Total revenues       121,722     91,854         203,437     160,453  
     

 

     

 

 
Costs and expenses:                                
    Cost of goods sold       15,612     12,631         31,261     19,582  
    Research and development       130,575     122,430         257,385     223,742  
    Selling, general and administrative       40,775     45,222         79,205     83,240  
    Restructuring charges       65,310             93,505      
    Acquired in-process research and development                       242,000  
    Amortization of intangibles       9,676     9,754         19,352     15,297  
     

 

     

 

 
        Total costs and expenses       261,948     190,037         480,708     583,861  
     

 

     

 

 
Loss from operations       (140,226 )   (98,183 )       (277,271 )   (423,408 )
                                 
Other income (expense):                                
    Investment income, net       8,697     14,893         18,304     43,050  
    Interest expense       (5,118 )   (10,449 )       (15,535 )   (17,242 )
    Gain on sale of equity interest in joint venture       40,000     40,000         40,000     40,000  
    Debt financing charge       (10,496 )   (54,000 )       (10,496 )   (54,000 )
     

 

     

 

 
Net loss     $ (107,143 ) $ (107,739 )     $ (244,998 ) $ (411,600 )
     

 

     

 

 
Amounts per common share:                                
Net loss per share, basic and diluted     $ (0.36 ) $ (0.38 )     $ (0.83 ) $ (1.53 )
     

 

     

 

 
Weighted average shares, basic and diluted       297,231     282,693         295,100     268,382  
     

 

     

 

 

See notes to condensed consolidated financial statements.

4


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

  Six Months Ended June 30,
 
  2003
  2002
 
(in thousands)    
                 
Cash Flows from Operating Activities:                
Net loss     $ (244,998 ) $ (411,600 )
Adjustments to reconcile net loss to cash                
used in operating activities:                
Acquired in-process research and development           242,000  
Depreciation and amortization       51,684     38,173  
Restructuring charges       71,804    
Amortization of deferred financing costs       11,956   561  
(Gain) loss on available-for-sale securities, net       (959 )   5,061  
Stock compensation expense       5,204     4,852  
Changes in operating assets and liabilities:                
  Accounts receivable       (8,031 )    
  Due from strategic alliance partners       (39,765 )   (13,370 )
  Inventory       (5,943 )    
  Prepaid expenses and other current assets       (41,890 )   (33,112 )
  Restricted cash and other assets       25,000     (6,276 )
  Accounts payable and accrued expenses       9,531     25,924  
  Deferred revenue       10,036     (25,555 )
     

 

 
Net cash used in operating activities       (156,371 )   (173,342 )
     

 

 
                 
Cash Flows from Investing Activities:                
Investments in marketable securities       (848,319 )   (690,685 )
Proceeds from sales and maturities of marketable securities       348,187     583,856  
Purchases of property and equipment and other long term assets       (38,851 )   (66,581 )
Net cash acquired in COR Therapeutics, Inc. acquisition           309,147  
Other investing activities       (704 )   (505 )
     

 

 
Net cash (used in) provided by investing activities       (539,687 )   135,232