<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549


                                    FORM 10-Q


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



                  FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2001



                         COMMISSION FILE NUMBER 0-12042



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



                MASSACHUSETTS                         04-3002117
         (State or other jurisdiction of            (I.R.S. Employer
         incorporation or organization)             Identification No.)



                    14 CAMBRIDGE CENTER, CAMBRIDGE, MA 02142
                                 (617) 679-2000
          (Address,including zip code, and telephone number, including
             area code, of registrant's principal executive offices)


         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 number of shares of the registrant's Common Stock, $0.01 par value,
         outstanding as of July 31, 2001 was 148,537,614 shares.


                                       1
<PAGE>   2
                                  BIOGEN, INC.

                                      INDEX

PART I - FINANCIAL INFORMATION                                       PAGE NUMBER

Condensed Consolidated Statements of Income - Three and
  six months ended June 30, 2001 and 2000                                 3

Condensed Consolidated Balance Sheets - June 30, 2001 and
  December 31, 2000                                                       4

Condensed Consolidated Statements of Cash Flows -
  Six months ended June 30, 2001 and 2000                                 5

Notes to Condensed Consolidated Financial Statements                      6

Management's Discussion and Analysis of Financial Condition
  and Results of Operations                                              10

PART II - OTHER INFORMATION                                              16





                           Note concerning trademarks:
               AVONEX(R) is a registered trademark of Biogen, Inc.


                                       2
<PAGE>   3
                          BIOGEN, INC. AND SUBSIDIARIES
                   CONDENSED CONSOLIDATED STATEMENTS OF INCOME
                                   (unaudited)
                    (in thousands, except per share amounts)



<TABLE>
<CAPTION>
                                         Three Months Ended      Six Months Ended
                                               June 30,              June 30,
                                           2001       2000       2001       2000
                                         --------   --------   --------   --------
<S>                                      <C>        <C>        <C>        <C>

REVENUES:
   Product                               $243,217   $190,009   $463,214   $364,605
   Royalties                               17,445     40,505     34,495     82,757
                                         --------   --------   --------   --------

Total revenues                            260,662    230,514    497,709    447,362
                                         --------   --------   --------   --------

COSTS AND EXPENSES:
   Cost of revenues                        35,202     30,795     64,348     59,418
   Research and development                79,118     71,701    151,888    134,707
   Selling, general and administrative     55,266     40,921    103,826     82,104
                                         --------   --------   --------   --------

Total costs and expenses                  169,586    143,417    320,062    276,229
                                         --------   --------   --------   --------

Income from operations                     91,076     87,097    177,647    171,133
Other income, net                          11,533     16,737     27,996    115,761
                                         --------   --------   --------   --------

INCOME BEFORE INCOME  TAXES               102,609    103,834    205,643    286,894
Income taxes                               30,757     31,774     61,668     93,468
                                         --------   --------   --------   --------

NET INCOME                               $ 71,852   $ 72,060   $143,975   $193,426
                                         ========   ========   ========   ========

BASIC EARNINGS PER SHARE                 $   0.48   $   0.48   $   0.97   $   1.29
                                         ========   ========   ========   ========
DILUTED EARNINGS PER SHARE               $   0.47   $   0.47   $   0.94   $   1.24
                                         ========   ========   ========   ========

SHARES USED IN COMPUTING:
Basic earnings per share                  148,602    148,643    148,395    149,501
                                         ========   ========   ========   ========
Diluted earnings per share                153,337    154,150    153,414    155,931
                                         ========   ========   ========   ========
</TABLE>







            See Notes to Condensed Consolidated Financial Statements.


                                       3
<PAGE>   4
                          BIOGEN, INC. AND SUBSIDIARIES
                      CONDENSED CONSOLIDATED BALANCE SHEETS
                                 (in thousands)

<TABLE>
<CAPTION>
                                                      June 30,      December 31,
                                                        2001            2000
                                                    -----------     -----------
                                                    (unaudited)
<S>                                                 <C>             <C>
ASSETS
Current assets
    Cash and cash equivalents                       $    75,972     $    48,737
    Marketable securities                               684,024         633,675
    Accounts receivable, net                            166,457         143,178
    Deferred tax assets                                  43,997          40,047
    Other current assets                                 56,683          62,634
                                                    -----------     -----------
    Total current assets                              1,027,133         928,271
                                                    -----------     -----------

Property, plant and equipment
    Cost                                                627,969         537,072
    Less accumulated depreciation                       153,865         136,643
                                                    -----------     -----------
    Property, plant and equipment, net                  474,104         400,429
                                                    -----------     -----------

Patents, net                                             15,086          13,510
Marketable securities                                    57,241          71,982
Other assets                                             20,332          17,664
                                                    -----------     -----------

                                                    $ 1,593,896     $ 1,431,856
                                                    ===========     ===========

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities

    Accounts payable                                $    49,239     $    37,869
    Current portion of long-term debt                     4,888           4,888
    Accrued expenses and other                          180,855         178,264
                                                    -----------     -----------
    Total current liabilities                           234,982         221,021
                                                    -----------     -----------

Long-term debt, less current portion                     44,741          47,185
Other long-term liabilities                              53,430          57,248
Commitments and contingencies                              --              --

Shareholders' equity

    Common stock                                          1,517           1,517
    Additional paid-in capital                          795,444         772,172
    Retained earnings                                   610,900         543,913
    Accumulated other comprehensive income               13,721          22,376
    Treasury stock, at cost                            (160,839)       (233,576)
                                                    -----------     -----------

Total shareholders' equity                            1,260,743       1,106,402
                                                    -----------     -----------
                                                    $ 1,593,896     $ 1,431,856
                                                    ===========     ===========
</TABLE>





            See Notes to Condensed Consolidated Financial Statements.


                                       4
<PAGE>   5
                          BIOGEN, INC. AND SUBSIDIARIES
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (unaudited)
                                 (in thousands)

<TABLE>
<CAPTION>
                                                                       Six Months Ended
                                                                           June 30,
                                                                       2001         2000
                                                                    ---------    ---------
<S>                                                                 <C>          <C>

CASH FLOWS FROM OPERATING ACTIVITIES
      Net income                                                    $ 143,975    $ 193,426
      Adjustments to reconcile net income to
         net cash provided from operating activities:
         Depreciation and amortization                                 18,070       16,321
         Deferred income taxes                                             86          268
         Tax benefit of stock options                                  22,622       67,377
         Other                                                            417        2,697
         Gain on sale of non-current marketable securities             (3,321)    (101,129)
         Changes in:
             Accounts receivable                                      (23,279)     (16,938)
             Other current and other assets                             3,962       (2,781)
             Accounts payable, accrued expense and
                other current and long-term liabilities                 9,687       22,263
                                                                    ---------    ---------
      Net cash from operating activities                              172,219      181,504
                                                                    ---------    ---------

CASH FLOWS FROM INVESTING ACTIVITIES
      Purchases of marketable securities                             (624,483)    (360,510)
      Proceeds from sales and maturities of marketable securities     575,863      374,940
      Proceeds from sales of non-current marketable securities          3,652      120,199
      Acquisitions of property and equipment                          (90,897)     (80,468)
      Additions to patents                                             (2,424)      (2,182)
                                                                    ---------    ---------
         Net cash from investing activities                          (138,289)      51,979
                                                                    ---------    ---------

CASH FLOWS FROM FINANCING ACTIVITIES
      Payments of long-term debt                                       (2,444)      (2,443)
      Purchases of treasury stock                                     (21,443)    (250,727)
      Issuance of common and treasury stock
         related to stock option exercises                             17,192       30,229
                                                                    ---------    ---------
         Net cash from investing activities                            (6,695)    (222,941)
                                                                    ---------    ---------

NET INCREASE IN CASH AND CASH EQUIVALENTS                              27,235       10,542

CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD                         48,737       56,920
                                                                    ---------    ---------

CASH AND CASH EQUIVALENTS, END OF PERIOD                            $  75,972    $  67,462
                                                                    =========    =========
</TABLE>






         See Notes to Condensed Consolidated Financial Statements.


                                       5
<PAGE>   6
                          BIOGEN, INC. AND SUBSIDIARIES
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (unaudited)


1.  BASIS OF PRESENTATION

In the opinion of management, the accompanying unaudited condensed consolidated
financial statements include all adjustments, consisting of only normal
recurring accruals, necessary to present fairly the financial position, results
of operations and cash flows of Biogen, Inc. and its subsidiaries (the
"Company"). The Company's accounting policies are described in the Notes to the
Consolidated Financial Statements in the Company's 2000 Annual Report on Form
10-K. Interim results are not necessarily indicative of the operating results
for the full year.

The preparation of financial statements in conformity with generally accepted
accounting principles requires management to make estimates and assumptions that
affect the reported amounts of assets and liabilities and disclosure of
contingent assets and liabilities at the date of the financial statements, and
the reported amounts of revenues and expenses during the reporting period.
Actual results could differ from those estimates. Certain amounts for the three
and six months ended June 30, 2000 have been reclassified to conform to the
current period presentation.


INVENTORIES

Inventories are stated at the lower of cost or market with cost determined under
the first-in/first-out ("FIFO") method and are included in other current assets.
Included in inventory are raw materials used in the production of pre-clinical
and clinical products which are expensed as research and development costs when
consumed. The components of inventories are as follows:

<TABLE>
<CAPTION>
                                                       June 30,   December 31,
(in thousands)                                           2001         2000
                                                       --------   ------------
<S>                                                    <C>          <C>

Raw materials                                          $ 11,484     $  7,775
Work in process                                          13,245       17,582
Finished goods                                           14,075       14,172
                                                       --------     --------
                                                       $ 38,804     $ 39,529
                                                       ========     ========
</TABLE>

2.  FINANCIAL INSTRUMENTS

On June 15, 1998, the Financial Accounting Standards Board issued Statement of
Financial Accounting Standards No. 133, "Accounting for Derivative Instruments
and Hedging Activities", ("SFAS 133"). The Company elected to adopt SFAS 133 in
the fourth quarter of 1998. All derivatives are recognized on the balance sheet
at their fair value. Changes in the fair value of derivatives are recorded each
period in current earnings or other comprehensive income, depending on whether a
derivative is designated as part of a hedge transaction and, if it is, the type
of hedge transaction. The Company assesses, both at its inception and on an
on-going basis, whether the derivatives that are used in hedging transactions
are highly effective in offsetting the changes in cash flows of hedged items.
The Company assesses hedge ineffectiveness on a quarterly basis and records the
gain or loss related to the ineffective portion to current earnings to the
extent significant. If the Company determines that a hedged forecasted
transaction is no longer probable of occurring, the Company discontinues hedge
accounting for the affected portion of the transaction, and any unrealized gain
or loss on the contract is recognized in current earnings.

As of June 30, 2001, the Company had $15.0 million outstanding under a floating
rate loan secured by one of the Company's laboratory and office buildings in
Cambridge, Massachusetts and $34.6 million outstanding under a floating rate
loan agreement for financing the construction of its biological manufacturing
facility in North Carolina. The Company uses interest rate swap agreements to
mitigate the risk associated with its floating rate debt. The fair value of the
interest rate swap agreements at June 30, 2001, representing the cash
requirements of the Company to settle the agreements, was approximately $2.2


                                       6
<PAGE>   7
million. The fair value of the interest rate swap agreements at June 30, 2000,
representing the cash the Company would receive to settle the agreements, was
approximately $561,000. The Company has designated the interest rate swaps as
cash flow hedges. There were no amounts of hedge ineffectiveness related to the
Company's interest rate swaps during the three and six months ended June 30,
2001 or in the comparable period of 2000, and no gains or losses were excluded
from the assessment of hedge effectiveness. The Company records the differential
to be paid or received on the interest rate swaps as incremental interest
expense.

The Company has foreign currency forward contracts to hedge specific forecasted
transactions denominated in foreign currencies. All foreign currency forward
contracts have durations of ninety days to 6 months. These contracts have been
designated as cash flow hedges and accordingly, to the extent effective, any
unrealized gains or losses on these foreign currency forward contracts are
reported in other comprehensive income. Realized gains and losses for the
effective portion are recognized with the underlying hedge transaction. The
notional amount of the foreign currency forward contracts outstanding at June
30, 2001 was approximately $49.2 million. These contracts had a fair value of
approximately $2.8 million, representing an unrealized gain, and were included
in other current assets at June 30, 2001.

For the three and six months ended June 30, 2001 and 2000, there were no
significant amounts recognized in earnings due to hedge ineffectiveness. For the
three and six months ended June 30, 2001, there were no significant amounts
recognized as a result of the discontinuance of cash flow hedge accounting
because it was no longer probable that the hedge forecasted transaction would
occur. For the three and six months ended June 30, 2000, approximately $388,000
and $392,000, respectively, in gains were recognized as a result of the
discontinuance of cash flow hedge accounting because it was no longer probable
that the hedge forecasted transaction would occur. The Company recognized $3.7
million and $6.7 million of gains in product revenue for the settlement of
certain effective cash flow hedge instruments for the three and six months
period ended June 30, 2001, respectively. The Company recognized $974,000 and
$1.8 million of gains in royalty revenue for the settlement of certain effective
cash flow hedge instruments for the three and six months period ended June 30,
2001, respectively. The Company recognized $2.3 million and $4.8 million of
gains in product revenue for the settlement of certain effective cash flow hedge
instruments for the three and six months period ended June 30, 2000,
respectively. The Company recognized $426,000 and $1.1 million of gains in
royalty revenue for the settlement of certain effective cash flow hedge
instruments for the three and six months period ended June 30, 2000,
respectively. These settlements were recorded in the same period as the related
forecasted transactions affecting earnings.

3.  COMPREHENSIVE INCOME

Comprehensive income is comprised of net income and other comprehensive income.
Other comprehensive income includes certain changes in equity that are excluded
from net income, such as translation adjustments and unrealized holding gains
and losses on available-for-sale marketable securities, net of tax and certain
derivative instruments, net of tax. Comprehensive income for the three months
ended June 30, 2001 and 2000 was $79.1 million and $77.1 million, respectively.
Comprehensive income for the six months ended June 30, 2001 and 2000 was $135.3
million and $177.4 million, respectively.

4.  EARNINGS PER SHARE

The Company calculates earnings per share in accordance with Statement of
Financial Accounting Standards No. 128, "Earnings per Share". Basic earnings per
share is computed by dividing the net income available to common shareholders by
the weighted average number of shares of common stock outstanding. For purposes
of calculating diluted earnings per share the denominator includes both the
weighted average number of shares of common stock outstanding and the number of
dilutive common stock equivalents such as stock options and warrants. Options to
purchase approximately 2.1 million and 1.7 million shares were outstanding at
June 30, 2001 and 2000, respectively, but not included in the computation of
diluted earnings per share because the options' exercise prices were greater
than the average market price during the period. The put warrants sold in


                                       7
<PAGE>   8
connection with the Company's stock repurchase program did not have a
significant additional dilutive effect. Shares used in calculating basic and
diluted earnings per share for the three and six month periods ending June 30,
are as follows:


<TABLE>
<CAPTION>
                                          Three Months Ended    Six Months Ended
                                                June 30,            June 30,
(in thousands)                               2001      2000      2001      2000
                                           -------   -------   -------   -------
<S>                                        <C>       <C>       <C>       <C>

Weighted average number of shares
      of common stock outstanding          148,602   148,643   148,395   149,501
Dilutive stock options                       4,735     5,507     5,019     6,430
                                           -------   -------   -------   -------
Shares used in calculating diluted
     earnings per share                    153,337   154,150   153,414   155,931
                                           =======   =======   =======   =======
</TABLE>


5.  SHARE REPURCHASE PROGRAM

On December 18, 2000, the Company announced that its Board of Directors had
authorized the repurchase of up to 4 million shares of the Company's common
stock. The repurchased stock will provide the Company with treasury shares for
general corporate purposes, such as stock to be issued under employee stock
option and stock purchase plans. Stock purchases are expected to occur from time
to time through out 2001. To enhance the 2000 stock repurchase program, the
Company entered into agreements with independent third parties under which the
Company committed to purchase up to 1,500,000 shares of the Company's stock
subject to the terms of the agreements at strike prices ranging from $57.82 to
$63.06. The Company purchased 328,000 shares through June 30, 2001 at a cost of
$21.4 million. The agreements permit a net share settlement at the Company's
option. In November of 2000, the Company completed a previous stock repurchase
program. During 2000, the Company repurchased approximately 4.6 million shares
of its common stock under this program at a cost of $300.2 million.

6.  OTHER INCOME, NET

Other income, net consists of the following (in thousands):

<TABLE>
<CAPTION>
                                 Three Months Ended          Six Months Ended
                                       June 30,                  June 30,
                               ----------------------    ----------------------
                                  2001         2000         2001         2000
                               ---------    ---------    ---------    ---------
<S>                            <C>          <C>          <C>          <C>

Interest income                $  10,694    $  10,370    $  22,479    $  21,107
Interest expense                  (1,051)      (1,080)      (2,089)      (2,185)
Other income                       1,890        7,447        7,606       96,839
                               ---------    ---------    ---------    ---------

Total other income, net        $  11,533    $  16,737    $  27,996    $ 115,761
                               =========    =========    =========    =========
</TABLE>


Other income for the three and six months ended June 30, 2001 includes gains on
the sale of certain non-current marketable securities totaling approximately
$781,000 and $3.3 million, respectively. Other income for the three and six
months ended June 30, 2000 includes gains on the sale of certain non-current
marketable securities totaling approximately $8.7 million and $101.1 million,
respectively.

7.  INCOME TAX EXPENSE

Income tax expense as a percentage of pre-tax income for the three months ended
June 30, 2001 and 2000 was approximately 30% and 31%, respectively. Income tax
expense as a percentage of pre-tax income for the six months ended June 30, 2001
and 2000 was approximately 30% and 33%, respectively. The effective tax rate
varied from the U.S. statutory rates for the first six months of 2001 and 2000
primarily due to higher sales in European jurisdictions with lower tax rates and
the utilization of research and development credits. The Company's effective tax
rate outside the U.S. is lower than the U.S. tax rate, and


                                       8
<PAGE>   9
the Company expects that the U.S. tax rate will decline as a percentage of its
total tax rate as international sales increase.

8.  LITIGATION

On July 3, 1996, Berlex Laboratories, Inc. ("Berlex") filed suit against Biogen
in the United States District Court for the District of New Jersey alleging
infringement by Biogen of Berlex's "McCormick" patent (U.S. Patent No.
5,376,567) in the United States in the production of Biogen's AVONEX(R)
(Interferon beta-1a) product. In November 1996, Berlex's New Jersey action was
transferred to the United States District Court in Massachusetts and
consolidated for pre-trial purposes with a related declaratory judgment action
previously filed by Biogen. On August 18, 1998, Berlex filed a second suit
against Biogen alleging infringement by Biogen of a patent which was issued to
Berlex in August 1998 and which is related to the McCormick patent (U.S. Patent
No. 5,795,779). On September 23, 1998, the cases were consolidated for pre-trial
and trial purposes. Berlex sought a judgment granting it damages, trebling of
any damages awarded and a permanent injunction restraining Biogen from the
alleged infringement. A hearing on the parties' summary judgment motions in the
case was completed in March 2000. In September 2000, the District Court rendered
final judgment in favor of Biogen and against Berlex determining that Biogen's
production of AVONEX(R) did not infringe any of the claims of the Berlex
patents. Berlex has appealed this decision to the Court of Appeals for the
Federal Circuit and the parties have briefed the appeal for oral argument. The
Company filed a contingent cross-appeal asserting that the Berlex patents are
invalid because they fail to meet one of the statutory requirements of
patentability. An unfavorable ruling on the appeal filed by Berlex could result
in the case being remanded to the District Court for trial. If Berlex were to be
successful in its appeal and the case were to be remanded, an unfavorable ruling
in the remanded case could have a material adverse effect on the Company's
results of operations and financial position. The Company believes that the
decision of the District Court that Biogen does not infringe the Berlex patents
is sound, but the ultimate outcome of the appeal is not currently determinable.
As a result, an estimate of any potential loss or range of loss cannot be made
at this time.

In 1995, the Company filed an opposition with the Opposition Division of the
European Patent Office to oppose a European patent (the "Rentschler I Patent")
issued to Dr. Rentschler Biotechnologie GmbH ("Rentschler") relating to
compositions of matter of beta interferon. In 1997, the European Patent Office
issued a decision to revoke the Rentschler I Patent. Rentschler appealed that
decision and an oral hearing on the appeal took place in December 2000. At the
oral hearing in order to gain reinstatement of the patent, Rentschler narrowed
the patent claims so as to claim only a specific cell line. Biogen does not use
the specific cell line now claimed. On October 13, 1998, the Company filed
another opposition with the Opposition Division of the European Patent Office to
oppose a second European patent issued to Rentschler (the "Rentschler II
Patent") with certain claims regarding compositions of matter of beta interferon
with specific regard to the structure of the glycosylated molecule. A hearing on
the Company's opposition may be held in 2001. While Biogen believes that the
Rentschler II Patent will be revoked, if the Rentschler II Patent were to be
upheld and if Rentschler were to obtain, through legal proceedings, a
determination that the Company's sale of AVONEX(R) in the European countries
giving effect to the patent infringes a valid claim of the patent, such result
could have a material adverse effect on the Company's results of operation and
financial position.

9.  SEGMENT INFORMATION

The chief operating decision makers review the profit and loss of the Company on
an aggregate basis and manage the operations of the Company as a single
operating segment. Accordingly, the Company operates in one segment, which is
the business of developing, manufacturing and marketing drugs for human health
care. The Company currently derives product revenues from sales of its AVONEX(R)
(Interferon beta-1a) product for the treatment of relapsing forms of multiple
sclerosis. The Company also derives revenue from royalties on worldwide sales by
the Company's licensees of a number of products covered under patents controlled
by the Company, including alpha interferon and hepatitis B vaccines and
diagnostic products.

10.  NEW ACCOUNTING PRONOUNCEMENT

In July 2001, the FASB issued SFAS No. 141, "Business Combinations" and SFAS No.
142, "Goodwill and Other Intangible Assets." SFAS No. 141 requires that all
business combinations be accounted for under the purchase method only and that
certain acquired intangible assets in a business combination be recognized as
assets apart from goodwill. SFAS No. 142 requires that ratable amortization of
goodwill be replaced with periodic tests of the goodwill's impairment and that
intangible assets other than goodwill be amortized over their useful lives. SFAS
No. 141 is effective for all business combinations initiated after June 30, 2001
and for all business combinations accounted for by the purchase method for which
the date of acquisition is after June 30, 2001. The provisions of SFAS No. 142
will be effective for fiscal years beginning after December 15, 2001, and will
thus be adopted by the Company, as required, in fiscal year 2002. The impact of
SFAS No. 141 and SFAS No. 142 on the Company's financial statements is not
expected to be material.


                                       9
<PAGE>   10
                          BIOGEN, INC. AND SUBSIDIARIES
         MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
                              RESULTS OF OPERATIONS


OVERVIEW

Biogen, Inc. (the "Company" or "Biogen") is a biopharmaceutical company
principally engaged in the business of developing, manufacturing and marketing
drugs for human health care. The Company currently derives revenues from sales
of its AVONEX(R) (Interferon beta-1a) product for the treatment of relapsing
forms of multiple sclerosis ("MS"). The Company also derives revenue from
royalties on worldwide sales by the Company's licensees of a number of products
covered under patents controlled by the Company, including alpha interferon and
hepatitis B vaccines and diagnostic products.


RESULTS OF OPERATIONS

For the quarter ended June 30, 2001, the Company reported net income of $71.9
million or $0.47 per diluted share as compared to $72.1 million or $0.47 per
diluted share for the comparable period of 2000. For the six months ended June
30, 2001, the Company reported net income of $144 million or $0.94 per diluted
share as compared to $193.4 million or $1.24 per diluted share for the
comparable period of 2000.

Total revenues for the quarter ended June 30, 2001 were $260.7 million, as
compared to $230.5 million in the same period of 2000, an increase of $30.2
million or approximately 13%. Total revenues for the six months ended June 30,
2001 were $497.7 million, as compared to $447.4 million in the same period of
2000, an increase of $50.3 million or approximately 11%.

Product revenues in the current quarter were $243.2 million as compared to $190
million for the same period of 2000, an increase of $53.2 million or
approximately 28%. Product revenues in the six months ended June 30, 2001 were
$463.2 million as compared to $364.6 million for the same period of 2000, an
increase of $98.6 million or approximately 27%. Product revenues from AVONEX(R)
represent approximately 93% of the Company's total revenues in the current
quarter and six months ended June 30, 2001 as compared to 82% for the three and
six month periods of 2000. The growth in the three and six month periods ended
June 30, 2001 over the comparable periods in 2000 was primarily attributable to
increases in the sales volume of AVONEX(R) in the United States and in the
fifteen member countries of the European Union ("EU"). AVONEX(R) sales outside
of the United States were approximately $70 million and $128.2 million in the
three and six months ended June 30, 2001 as compared to $51.2 million and $99.5
million in the same periods of 2000, respectively.

Revenues from royalties in the three months ended June 30, 2001 were $17.4
million, a decrease of $23.1 million or approximately 57% as compared to $40.5
million of royalty revenue for the same period in 2000. Revenues from royalties
in the six months ended June 30, 2001 were $34.5 million, a decrease of
approximately 58% as compared to $82.8 million of royalty revenue for the same
period in 2000. Revenues from royalties represented approximately 7% of total
revenues for the three and six months ended June 30, 2001 as compared to 18% for
the same periods in 2000.

COSTS AND EXPENSES

Total costs and expenses for the three months ended June 30, 2001 were $169.6
million as compared to $143.4 million in the same period of 2000, an increase of
approximately 18%. Total costs and expenses for the six months ended June 30,
2001 were $320.1 million as compared to $276.2 million in the same period of
2000, an increase of approximately 16%.

Cost of revenues in the three months ended June 30, 2001 totaled $35.2 million
compared to $30.8 million in the same period of 2000, an increase of $4.4
million or 14%. Cost of revenues in the six months ended June 30, 2001 totaled
$64.3 million compared to $59.4 million in the same period of 2000, an increase
of $4.9 million or 8%. The increase in cost of revenues was attributable to the
higher sales volume of


                                       10
<PAGE>   11
AVONEX(R). Included in cost of revenues for the three months ended June 30, 2001
and 2000 is $33.9 million and $27.5 million, respectively, of costs related to
product revenues and $1.3 million and $3.3 million, respectively, of costs
related to royalty revenue. Included in cost of revenues for the six months
ended June 30, 2001 and 2000 is $62.2 million and $53.5 million, respectively,
of costs related to product revenues and $2.1 million and $5.9 million,
respectively, of costs related to royalty revenue. Gross margins on product
revenues remained constant at approximately 86% for the three months ended June
30, 2001 compared to the same period in 2000. Gross margins on product revenues
increased to approximately 87% for the six months ended June 30, 2001 compared
to 85% in the same period in 2000. Gross margins on royalty revenue increased to
approximately 93% for the three months ended June 30, 2001 compared to 92% for
the same period in 2000. Gross margins on royalty revenue increased to
approximately 94% for the six months ended June 30, 2001 compared to 93% in the
same period in 2000. The Company expects that gross margins on royalty revenue
will fluctuate in the future based on changes in sales volumes for specific
products.

Research and development expenses in the current quarter were $79.1 million, an
increase of $7.4 million or 10% as compared to $71.7 million in the same period
of 2000. Research and development expenses in the six months ended June 30, 2001
were $151.9 million, an increase of $17.2 million or 13% as compared to $134.7
million in the same period of 2000. The increase was primarily due to an
increase in clinical trial costs and the costs associated with an increase in
the Company's other development efforts related to its ongoing research and
development programs. The Company expects that, in the near and long-term,
research and development expenses will increase as the Company continues to
expand its development efforts with respect to new products, conducts clinical
trials of these products and continues work on new formulations and delivery
methods for AVONEX(R).

Selling, general and administrative expenses in the second quarter of 2001 were
$55.3 million, an increase of $14.4 million or 35% as compared to the same
period of 2000. Selling, general and administrative expenses in the six months
ended June 30, 2001 were $103.8 million, an increase of $21.7 million or 26%
compared to the same period of 2000. This increase was primarily due to an
increase in selling and marketing expenses related to the sale of AVONEX(R). The
Company expects that selling, general and administrative expenses will continue
to increase in the near term as the Company continues to expand its sales and
marketing organizations and efforts necessary to sell AVONEX(R) worldwide.

OTHER INCOME, NET

Other income, net consists primarily of interest income, partially offset by
interest expenses and other non-operating income and expenses. Other income, net
in the current quarter of 2001 was $11.5 million as compared to $16.7 million in
2000, a decrease of $5.2 million. Other income, net in the six months ended June
30, 2001 was $28 million as compared to $115.8 million in 2000, a decrease of
$87.8 million. Interest income for the three months ended June 30, 2001 was
$10.7 million compared to $10.4 million in the same period of 2000, an increase
of $0.3 million or 3%. Interest income for the first six months of 2001 was
$22.5 million compared to $21.1 million in the same period of 2000, an increase
of $1.4 million or 7% due primarily to higher average yields and an increase in
funds invested. The Company expects interest income to vary based on changes in
the amount of funds invested and fluctuations in interest rates. In the three
months ended June 30, 2001 interest expense was $1.1 million, comparable to the
same period in 2000. In the six months ended June 30, 2001 interest expense
decreased to $2.1 million from $2.2 million compared to the same period in 2000.
Other income for the three and six months ended June 30, 2001 includes gains on
the sale of certain non-current marketable securities totaling approximately
$781,000 and $3.3 million, respectively. Other income decreased by $5.6 million
in the first three months of 2001 from the same period in 2000. Other income
decreased by $89.2 million in the six months ended June 30, 2001 from the same
period in 2000. The decrease in other income is due primarily to the sale of
certain non-current marketable securities generating gains of approximately $8.7
million and $101.1 million in the three and six months ended June 30, 2000.


                                       11
<PAGE>   12
Other income, net consists of the following (in thousands):

<TABLE>
<CAPTION>
                                Three Months Ended          Six Months Ended
                                      June 30,                   June 30,
                               ----------------------    ----------------------
                                  2001         2000         2001         2000
                               ---------    ---------    ---------    ---------
<S>                            <C>          <C>          <C>          <C>
Interest income                $  10,694    $  10,370    $  22,479    $  21,107
Interest expense                  (1,051)      (1,080)      (2,089)      (2,185)
Other income (expense)             1,890        7,447        7,606       96,839
                               ---------    ---------    ---------    ---------

Total other income, net        $  11,533    $  16,737    $  27,996    $ 115,761
                               =========    =========    =========    =========
</TABLE>


INCOME TAXES

Income tax expense as a percentage of pre-tax income for the three months ended
June 30, 2001 and 2000 was approximately 30% and 31%, respectively. Income tax
expense as a percentage of pre-tax income for the six months ended June 30, 2001
and 2000 was approximately 30% and 33%, respectively. During the three and six
months ended June 30, 2001 and 2000, the Company recognized gains on the sale of
certain non-current marketable securities. Excluding the tax effect on these
gains the Company's effective tax rate for the three and six months ended June
30, 2001 and 2000 was approximately 30%. The effective tax rate varied from the
U.S. statutory rates for the first six months of 2001 and 2000 primarily due to
higher sales in European jurisdictions with lower tax rates and the utilization
of research and development credits. The Company's effective tax rate outside
the U.S. is lower than the U.S. tax rate, and the Company expects that the U.S.
tax rate will decline as a percentage of its total tax rate as international
sales increase.

FINANCIAL CONDITION

At June 30, 2001, cash, cash equivalents and short-term marketable securities
were $760 million compared with $682.4 million at December 31, 2000, an increase
of $77.6 million. Working capital increased $84.9 million to $792.2 million. Net
cash from operating activities for the period ended June 30, 2001 was $172.2
million compared with $181.5 million for the same period in 2000. Cash outflows
from investing activities during the first six months of 2001 included
investments in property and equipment and patents of $93.3 million. Net cash
outflows from investing activities related to marketable securities was $45
million. Significant cash outflows from financing activities included $21.4
million for purchases of the Company's common stock under its stock repurchase
program and $2.4 million for repayments on loan agreements with banks. Cash
inflows included $17.2 million from common stock option exercises and employee
stock purchase plan activity.

On December 18, 2000, the Company announced that its Board of Directors had
authorized the repurchase of up to 4 million shares of the Company's common
stock. The repurchased stock will provide the Company with treasury shares for
general corporate purposes, such as stock to be issued under employee stock
option and stock purchase plans. Stock purchases are expected to occur from time
to time through out 2001. To enhance the 2000 stock repurchase program, the
Company entered into agreements with independent third parties under which the
Company committed to purchase up to 1,500,000 shares of the Company's stock
subject to the terms of the agreements at strike prices ranging from $57.82 to
$63.06. The Company purchased 328,000 shares through June 30, 2001 at a cost of
$ 21.4 million. The agreements permit a net share settlement at the Company's
option. In November of 2000, the Company completed a previous stock repurchase
program. During 2000, the Company repurchased approximately 4.6 million shares
of its common stock under this program at a cost of $300.2 million.

On October 4, 1999, the Company began construction of its new research and
development center in Cambridge, Massachusetts. The new 224,000 square foot
building was completed in the spring of 2001 at a total cost of approximately
$95 million, of which $87.7 million had been committed at June 30, 2001.
Additionally, the Company is building a large scale manufacturing plant in
Research Triangle Park, North Carolina. The Company expects that construction
will be completed at the end of 2001 at a total cost of approximately $175
million, of which $164 million had been committed at June 30, 2001.


                                       12
<PAGE>   13
Several legal proceedings were pending during the current quarter, which involve
the Company. See Note 8 of the Notes to the Condensed Consolidated Financial
Statements. See also Item 1 - Business, "Patents and Other Proprietary Rights"
of the Company's Annual Report on Form 10-K for the fiscal year ended December
31, 2000 for discussions of these legal proceedings.

The Company believes that existing funds and cash generated from operations are
adequate to satisfy its working capital and capital expenditure requirements in
the foreseeable future. However, the Company may raise additional capital to
take advantage of favorable conditions in the market or in connection with the
Company's development activities.

NEW ACCOUNTING PRONOUNCEMENT

In July 2001, the FASB issued SFAS No. 141, "Business Combinations" and SFAS No.
142, "Goodwill and Other Intangible Assets." SFAS No. 141 requires that all
business combinations be accounted for under the purchase method only and that
certain acquired intangible assets in a business combination be recognized as
assets apart from goodwill. SFAS No. 142 requires that ratable amortization of
goodwill be replaced with periodic tests of the goodwill's impairment and that
intangible assets other than goodwill be amortized over their useful lives. SFAS
No. 141 is effective for all business combinations initiated after June 30, 2001
and for all business combinations accounted for by the purchase method for which
the date of acquisition is after June 30, 2001. The provisions of SFAS No. 142
will be effective for fiscal years beginning after December 15, 2001, and will
thus be adopted by the Company, as required, in fiscal year 2002. The impact of
SFAS No. 141 and SFAS No. 142 on the Company's financial statements is not
expected to be material.

OUTLOOK

SAFE HARBOR STATEMENT UNDER PRIVATE SECURITIES LITIGATION REFORM ACT OF 1996

In addition to historical information, this quarterly report contains
forward-looking statements that involve risks and uncertainties that could cause
actual results to differ materially from those reflected in such forward-looking
statements. Reference is made in particular to forward-looking statements
regarding the anticipated level of future product sales, royalty revenues,
expenses and profits and predictions as to the anticipated outcome of pending
litigation and patent-related proceedings. These and all other forward-looking
statements are made based on the Company's current belief as to the outcome and
timing of such future events. Factors which could cause actual results to differ
from the Company's expectations and which could negatively impact the Company's
financial condition and results of operations are discussed below and elsewhere
in this Management's Discussion and Analysis of Financial Condition and Results
of Operations.

DEPENDENCE ON AVONEX(R) SALES

The Company's ability to sustain increases in revenues and profitability in the
near term will be primarily dependent on the level of revenues and profitability
from AVONEX(R) sales. The Company's ability to sustain profitability from sales
of AVONEX(R) will depend on a number of factors, including: continued market
acceptance of AVONEX(R) worldwide; the Company's ability to maintain a high
level of patient satisfaction with AVONEX(R); the nature of regulatory and
pricing decisions related to AVONEX(R) worldwide; the extent to which
AVONEX(R) receives and maintains reimbursement coverage; successful resolution
of the lawsuit with Berlex related to the "McCormick" patents, which if
ultimately decided in Berlex's favor could have a material adverse effect on the
Company's financial position and results of operations; success in revoking the
Rentschler patent since if the patent were to be upheld and if Rentschler were
to obtain, through legal proceedings, a determination that the Company's sale of
AVONEX(R) in Europe infringes a valid Rentschler patent, such result could have
a material adverse effect on the Company's results of operation and financial
condition; the success of ongoing development work related to AVONEX(R) in
expanded MS indications; the continued accessibility of third parties to vial,
label, and distribute AVONEX(R) on acceptable terms; and the Company's ability
to sustain market share of AVONEX(R) in light of the impact of competitive
products for the treatment of MS. In the United States, one of the Company's
competitors, Serono Laboratories, Inc. ("Serono"), is conducting a 12-month
head-to-head study of Rebif(R), a recombinant interferon beta-1a product and
AVONEX(R) to determine if Rebif(R) is clinically superior to AVONEX(R).
Preliminary results of the study were released by Serono in the second quarter
of 2001. At that time Serono stated that it will use the results of this study
in its attempts to overcome the orphan drug status of AVONEX(R) and to get
Rebif(R) approved before expiration of AVONEX's(R) orphan drug status. If
Serono is successful, competition in the United States multiple sclerosis
marketplace will increase.

ROYALTY REVENUE

The Company receives royalty revenues which contribute a significant amount to
its overall profitability. The Company expects to continue to experience a
decline in royalty revenues as a result of patent expirations and other
patent-related events in the range of up to approximately $10 million per
quarter for 2001 (not including amounts that are subject to a royalty dispute
with Schering-Plough Corporation ("Schering-Plough") as discussed below). See
"Outlook - Patents and Other Proprietary Rights" in the Company's Annual Report
on Form 10-K for the


                                       13
<PAGE>   14
period ended December 31, 2000. The Company expects the most significant decline
to be in the amount of royalties received from Schering-Plough on sales of
INTRON(R) A as the result of patent expirations in the EU and Japan and the
royalty dispute with Schering-Plough in the United States. The extent of the
decline in royalties related to United States sales of INTRON(R) A will depend
on the outcome of a dispute with Schering-Plough. Schering-Plough has taken the
position that a Court of Appeals' decision narrowing the scope of the claims of
Biogen's United States alpha interferon patent (the "901 Patent") permits it to
discontinue payment of royalties on U.S. sales of its alpha interferon products.
Biogen has filed for arbitration to compel payment of unpaid past royalties and
to ensure payment of royalties due in the future under a license agreement.
Given Schering-Plough's history of taking aggressive positions in contract
interpretation, Biogen has included claims which would resolve issues related to
future royalty payments to pre-empt any potential challenges by Schering-Plough.
These claims include Schering-Plough's obligation to commence royalty payments
in July 2002 (the expiration date of the 901 Patent) based on a patent
application owned by F. Hoffman-LaRoche ("Roche") and Genentech, Inc.
("Genentech"). The agreement between Biogen and Schering-Plough extending
Schering-Plough's royalty obligation beyond the expiration date of the 901
Patent was part of the settlement of a lawsuit between Biogen and
Roche/Genentech. In return for Schering-Plough's agreement to extend its royalty
obligation, Biogen settled the lawsuit with Roche/Genentech and Roche granted
Schering Plough an exclusive license for Schering-Plough to sell its products
under the Roche/Genentech patent right that was the subject of the dispute.
Biogen intends to vigorously oppose Schering-Plough's attempts to discontinue
payment of royalties. If Schering-Plough were to prevail in arbitration, the
resulting decline in royalties on United States sales of alpha interferon
products will range up to approximately an additional $10 million per quarter
until July 2002.

There are a number of other factors which could also cause the actual level of
royalty revenue to differ from the Company's expectations. For example, pricing
reforms, health care reform initiatives, other legal and regulatory developments
and the introduction of competitive products may have an impact on product sales
by the Company's licensees. In addition, sales levels of products sold by the
Company's licensees may fluctuate from quarter to quarter due to the timing and
extent of major events such as new indication approvals or government sponsored
programs. Since the Company is not involved in the development or sale of
products by its licensees, the Company can not be certain of the timing or
potential impact of factors which may affect sales by the Company's licensees.
In the long term, the Company expects its royalty revenue to be affected most
significantly by patent expirations and a potential decrease in sales by
licensees of licensed products. See "Outlook - Patents and Other Proprietary
Rights."

There can be no assurance that the Company will achieve a positive outcome with
respect to any of the factors discussed in this Section or that the timing and
extent of the Company's success with respect to any combination of these factors
will be sufficient to result in sustained increases in revenues or profitability
or the sustained profitability of the Company. For a further discussion of risks
regarding drug development, patent matters, including the Berlex lawsuit on the
"McCormick" patents and the Amgen appeal, competition in the MS market and
regulatory matters, see the Company's Annual Report on Form 10-K for the period
ended December 31, 2000 under the headings "Business - Risks Associated with
Drug Development", "Business - Patents and Other Proprietary Rights", "Business
- Competition and Marketing - AVONEX(R) (interferon beta-1a)", "Business -
Regulation", "Legal Proceedings" and "Management's Discussion and Analysis of
Financial Condition and Results of Operations - Outlook."

PRODUCTS

AVONEX(R) is currently the only product sold by the Company. The Company's
long-term viability and growth will depend on the successful development and
commercialization of other products from its research activities and
collaborations. The Company continues to expand its development efforts related
to other potential products in its pipeline. The expansion of the pipeline may
include increases in spending on internal projects, the acquisition of
third-party technologies or products or other types of investments. Product
development involves a high degree of risk. Only a small number of research and
development programs result in the commercialization of a product. Success in
preclinical and early clinical trials does not ensure that later stage or large
scale clinical trials will be successful. Many important factors affect the
Company's ability to successfully develop and commercialize drugs, including the
ability to obtain and maintain necessary patents and licenses, to demonstrate
safety and efficacy of drug candidates at each stage


                                       14
<PAGE>   15
of the clinical trial process, to overcome technical hurdles that may arise, to
meet applicable regulatory standards, to receive required regulatory approvals,
to be capable of producing drug candidates in commercial quantities at
reasonable costs, to obtain reimbursement coverage for the products, to compete
successfully against other products and to market products successfully. There
can be no assurance that the Company will be successful in its efforts to
develop and commercialize new products.

Patents and Other Proprietary Rights

The Company has numerous issued patents and patent applications pending on a
number of its processes and products. The Company has also obtained rights to
certain patents under licenses with third parties which provide for the payment
of royalties. There can be no assurance that the Company's existing patents or
others, if obtained, will provide substantial protection or commercial benefit
to the Company. In addition, the Company does not know to what extent its
pending patent applications or patent applications licensed from third parties
will be granted or whether any of its patents will prevail if they are
challenged in litigation. Also, there can be no assurance that third parties
will not be granted patents claiming subject matter necessary to the Company's
business. The Company is aware of certain patents held by Genentech relating to
immunoadhesion technology that may cover the Company's AMEVIVE(TM) product. The
Company has had discussions with Genentech regarding licensing and is evaluating
these patents to determine if a license should be taken.

The Company has granted an exclusive worldwide license to Schering-Plough under
its alpha interferon patents. Schering-Plough's royalty obligation to the
Company under these patents is discussed above in "Royalty Revenue".

The Company has licensed its recombinant hepatitis B antigen patent rights to
manufacturers and marketers of hepatitis B vaccines and diagnostic test kits,
and receive royalties on sales of the vaccines and test kits by the Company's
licensees. The obligation of SmithKline Beecham Biological S.A. and Merck & Co.,
Inc. to pay royalties on sales of hepatitis B vaccines and the obligation of the
Company's other licensees under the Company's hepatitis B patents to pay
royalties on sales of diagnostic products will terminate upon expiration of the
Company's hepatitis B patents. In August 2001 a United States patent was issued
to the Company covering a pharmaceutical composition for stimulating production
of antibodies in humans against a hepatitis B virus, a method of using the
pharmaceutical composition, a diagnostic kit for detecting antibodies against a
hepatitis B virus, and an in vitro method for detecting antibodies against a
hepatitis B virus. This patent will expire in 2018. The Company's European
hepatitis B patents expired at the end of 1999, except in those countries in
which the Company obtained supplemental protection certificates. The Company has
received supplemental protection certificates in Australia, Belgium, France,
Great Britain, Ireland, Italy, Luxembourg, The Netherlands, Sweden and
Switzerland, and has a number of granted or pending registrations of the Great
Britain supplementary protection certificates in various British territories.
The additional coverage afforded by supplemental protection certificates, or
related registrations, ranges from two to eight years. There can be no assurance
as to the extent of coverage available under the supplemental protection
certificates, or that protection will be available in additional countries.


                                       15


<PAGE>   16
PART II - OTHER INFORMATION

Item 4 - Submission of Matters to a Vote of Security Holders

(a)      The information set forth in this Item 4 relates to matters submitted
         to a vote at the Annual Meeting of Stockholders of Biogen, Inc. on June
         15, 2001.

(b)      Not applicable.

(c)      A proposal to elect Alan Belzer, Mary L. Good, Sir Kenneth Murray and
         James W. Stevens as directors to serve for a three year term ending in
         2004 and until their successors are duly elected and qualified was
         approved with the following vote:

<TABLE>
<CAPTION>
         Nominee                    For                    Abstains
         -------                    ---                    --------
<S>                                 <C>                    <C>
         Alan Belzer                119,822,165            956,941
         Mary L. Good               119,787,484            991,622
         Sir Kenneth Murray         119,796,502            982,604
         James W. Stevens           119,816,288            962,818
</TABLE>


         A proposal to ratify the selection of PricewaterhouseCoopers LLP as the
         Company's independent accountants for the fiscal year ending December
         31, 2001 was approved with 119,668,561 affirmative votes, 632,723
         negative votes, and 477,822 abstentions.

(d)      Not applicable.

Item 5 - Other Information

None.

Item 6 - Exhibits and Reports on Form 8-K

(a)      Exhibits

No. 10   1985 Non-Qualified Stock Option Plan (as amended and restated through
         April 27, 2001).

(b)      None.



                                       16
<PAGE>   17
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.


                                  BIOGEN, INC.

Dated: August 14, 2001             /s/ Peter N. Kellogg
                                  -----------------------------------------
                                  Vice President - Finance and
                                   Chief Financial Officer




                                       17