<PAGE>   1


                    U.S. SECURITIES AND EXCHANGE COMMISSION

                             WASHINGTON, D.C. 20549


                                    FORM 10-Q



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

              For the quarterly period ended June 30, 2000

/ /      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 0-19267

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

          PENNSYLVANIA                                          23-2472830
 (State or other jurisdiction of                             (I.R.S. Employer
 incorporation or organization)                             Identification No.)

     64 Sidney Street, Cambridge, MA                             02139-4136
   (Address of principal executive offices)                      (Zip Code)

Registrant's telephone number including area code:  (617) 494-0171

                                 Not Applicable
             (Former name, former address, and former fiscal year,
                          if changed since last report)

         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 the number of shares outstanding of each of the issuer's
classes of common stock, as of the latest practicable date.

           Class                        Shares Outstanding as of August 8, 2000
           -----                        ----------------------------------------
  Common Stock, par value $.01                       54,579,339
    Non-Voting Common Stock,
          par value $.01                                382,632
<PAGE>   2
                         ALKERMES, INC. AND SUBSIDIARIES


                                      INDEX
<TABLE>
<CAPTION>


                                                                                                    Page No.
                                                                                                    --------
<S>                                                                                                 <C>
PART I - FINANCIAL INFORMATION

                Item 1.    Consolidated Financial Statements

                           Consolidated Balance Sheets                                                    3
                           - June 30, 2000 and March 31, 2000

                           Consolidated Statements of Operations                                          4
                           - Three months ended June 30, 2000 and 1999

                           Consolidated Statement of Shareholders' Equity                                 5
                           - Three months ended June 30, 2000

                           Consolidated Statements of Cash Flows                                          6
                           - Three months ended June 30, 2000 and 1999

                           Notes to Consolidated Financial Statements                                     7

                Item 2.    Management's Discussion and Analysis of                                        9
                           Financial Condition and Results of Operations

                Item 3.    Quantitative and Qualitative Disclosures About Market Risk                     12

PART II - OTHER INFORMATION

                Item 4.    Submission of Matters to a Vote of Security Holders                            14

                Item 6.    Exhibits and Reports on Form 8-K                                               15

SIGNATURES                                                                                                17

EXHIBIT INDEX                                                                                             18

</TABLE>

                                      (2)
<PAGE>   3
PART I.  FINANCIAL INFORMATION

ITEM 1.  CONSOLIDATED FINANCIAL STATEMENTS:

                         ALKERMES, INC. AND SUBSIDIARIES

                           CONSOLIDATED BALANCE SHEETS
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                                                          June 30,              March 31,
                                                                                            2000                  2000
                                                                                       -------------          -------------
<S>                                                                                    <C>                    <C>
                     A S S E T S
Current Assets:
      Cash and cash equivalents                                                        $   5,490,054          $   6,100,643
      Short-term investments                                                             321,918,126            331,266,720
      Receivables from collaborative arrangements                                         30,599,612              3,182,382
      Prepaid expenses and other current assets                                            6,639,169              5,291,701
                                                                                       -------------          -------------
           Total current assets                                                          364,646,961            345,841,446
                                                                                       -------------          -------------
Property, Plant and Equipment:
      Land                                                                                   235,000                235,000
      Building                                                                             3,602,755              3,538,935
      Furniture, fixtures and equipment                                                   37,199,261             35,845,461
      Leasehold improvements                                                              13,733,194             13,804,269
                                                                                       -------------          -------------
                                                                                          54,770,210             53,423,665
           Less accumulated depreciation and amortization                                (21,931,195)           (20,554,182)
                                                                                       -------------          -------------
                                                                                          32,839,015             32,869,483
                                                                                       -------------          -------------
Investments                                                                               14,124,232             20,094,438
                                                                                       -------------          -------------
Other Assets                                                                              15,182,047             15,155,738
                                                                                       -------------          -------------
      Total Assets                                                                     $ 426,792,255          $ 413,961,105
                                                                                       =============          =============
   L I A B I L I T I E S  A N D  S H A R E H O L D E R S'  E Q U I T Y

Current Liabilities:
      Accounts payable and accrued expenses                                            $   8,445,617          $   7,227,897
      Accrued interest                                                                     2,850,145                979,497
      Deferred revenue                                                                     8,455,027              8,655,062
      Long-term obligations-current portion                                                5,550,000              5,625,000
                                                                                       -------------          -------------
           Total current liabilities                                                      25,300,789             22,487,456
                                                                                       -------------          -------------
Long-Term Obligations                                                                     21,441,625             22,791,625
                                                                                       -------------          -------------
Convertible Subordinated Notes                                                           200,000,000            200,000,000
                                                                                       -------------          -------------
Other Long-Term Liabilities                                                                  811,247                715,029
                                                                                       -------------          -------------
Shareholders' Equity
      Capital stock, par value $.01 per share:  authorized, 2,250,000 shares;
        none issued
      Convertible exchangeable preferred stock, par value $.01 per share:
        authorized and issued, 2,300,000 shares; outstanding, 2,298,925
        and 2,299,000 shares at June 30, 2000 and March 31, 2000, respectively
        (liquidation preference of $114,946,250)                                              22,989                 22,990
      Common stock, par value $.01 per share:
        authorized, 160,000,000 shares; issued, 53,976,339 and
        53,953,996 shares at June 30, 2000 and March 31, 2000, respectively                  539,764                539,540
      Non-voting common stock, par value $.01 per share:
        authorized, 450,000 shares; issued, 382,632 at June 30, 2000 and
        March 31, 2000, respectively                                                           3,826                  3,826
      Additional paid-in capital                                                         428,374,519            427,577,936
      Deferred compensation                                                               (6,085,945)            (8,545,926)
      Accumulated other comprehensive income                                               6,860,206              6,742,064
      Accumulated deficit                                                               (250,476,765)          (258,373,435)
                                                                                       -------------          -------------
           Total shareholders' equity                                                    179,238,594            167,966,995
                                                                                       -------------          -------------
           Total Liabilities and Shareholders' Equity                                  $ 426,792,255          $ 413,961,105
                                                                                       =============          =============
</TABLE>


See notes to consolidated financial statements


                                      (3)
<PAGE>   4
                         ALKERMES, INC. AND SUBSIDIARIES

                      CONSOLIDATED STATEMENTS OF OPERATIONS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                                              Three Months          Three Months
                                                                  Ended                Ended
                                                                June 30,             June 30,
                                                                  2000                 1999
                                                              ------------          ------------
<S>                                                           <C>                   <C>
Revenues:
     Research and development revenue under
        collaborative arrangements                            $ 28,966,945          $  5,762,521
                                                              ------------          ------------
Expenses:
     Research and development                                   14,439,893            12,270,006
     General and administrative                                  4,816,957             3,435,992
     Noncash compensation expense                                3,149,334                62,197
                                                              ------------          ------------
           Total expenses                                       22,406,184            15,768,195
                                                              ------------          ------------
Net operating income (loss)                                      6,560,761           (10,005,674)
                                                              ------------          ------------
Other income (expense):
     Interest income                                             5,598,966             2,459,989
     Interest expense                                           (2,395,180)             (743,154)
                                                              ------------          ------------
                                                                 3,203,786             1,716,835
                                                              ------------          ------------
Net income (loss)                                                9,764,547            (8,288,839)

Preferred stock dividends                                       (1,867,877)           (2,098,714)
                                                              ------------          ------------

Net income (loss) attributable to common shareholders         $  7,896,670          $(10,387,553)
                                                              ============          ============
Earnings (loss) per common share:
     Basic                                                    $       0.15          $      (0.21)
                                                              ============          ============

     Diluted                                                  $       0.13          $      (0.21)
                                                              ============          ============

Weighted average common shares used to
     compute earnings (loss) per common share:
     Basic                                                      53,957,017            50,079,254
                                                              ============          ============

     Diluted                                                    59,856,383            50,079,254
                                                              ============          ============
</TABLE>


See notes to consolidated financial statements.


                                      (4)
<PAGE>   5

                         ALKERMES, INC. AND SUBSIDIARIES

                 CONSOLIDATED STATEMENT OF SHAREHOLDERS' EQUITY
                                   (Unaudited)
<TABLE>
<CAPTION>


                                                  $3.25 Convertible
                                                     Exchangeable                                             Non-voting
                                                   Preferred Stock               Common Stock                Common Stock
                                                 Shares        Amount        Shares         Amount       Shares        Amount
-----------------------------------------------------------------------------------------------------------------------------------
<S>                                       <C>             <C>             <C>             <C>            <C>          <C>
Balance, April 1, 2000                     2,299,000       $  22,990       53,953,996      $ 539,540      382,632      $ 3,826

Issuance of common stock                          --              --           22,091            221           --           --

Conversion of $3.25 convertible
  exchangeable preferred stock                   (75)             (1)             252              3           --           --

Noncash compensation                              --              --               --             --           --           --

Amortization of noncash compensation              --              --               --             --           --           --

Unrealized gain on marketable securities          --              --               --             --           --           --

Cumulative foreign currency translation
  adjustments                                     --              --               --             --           --           --

Net income for period                             --              --               --             --           --           --

Preferred stock dividends                         --              --               --             --           --           --
                                           ---------       ---------       ----------      ---------      -------      -------
Balance, June 30, 2000                     2,298,925       $  22,989       53,976,339      $ 539,764      382,632      $ 3,826
                                           =========       =========       ==========      =========      =======      =======
</TABLE>


<TABLE>
<CAPTION>

                                                                                        Other Comprehensive
                                                                                           Income (Loss)
                                                                                 -----------------------------------
                                             Additional                          Foreign Currency    Unrealized Gain
                                               Paid-in          Deferred           Translation        on Marketable
                                               Capital        Compensation         Adjustments         Securities
--------------------------------------------------------------------------------------------------------------------
<S>                                       <C>              <C>                 <C>                  <C>
Balance, April 1, 2000                     $ 427,577,936    $  (8,545,926)      $  (64,686)          $ 6,806,750

Issuance of common stock                         107,232               --               --                    --

Conversion of $3.25 convertible
  exchangeable preferred stock                        (2)              --               --                    --

Noncash compensation                             689,353         (689,353)              --                    --

Amortization of noncash compensation                  --        3,149,334               --                    --

Unrealized gain on marketable securities              --               --               --               145,250

Cumulative foreign currency translation
  adjustments                                         --               --          (27,108)                   --

Net income for period                                 --               --               --                    --

Preferred stock dividends                             --               --               --                    --
                                           -------------    -------------       ----------           -----------
Balance, June 30, 2000                     $ 428,374,519    $  (6,085,945)      $  (91,794)          $ 6,952,000
                                           =============    =============       ==========           ===========
</TABLE>


<TABLE>
<CAPTION>

                                             Accumulated
                                               Deficit               Total
-----------------------------------------------------------------------------
<S>                                        <C>                 <C>
Balance, April 1, 2000                      $(258,373,435)      $ 167,966,995

Issuance of common stock                               --             107,453

Conversion of $3.25 convertible
  exchangeable preferred stock                         --                  --

Noncash compensation                                   --                  --

Amortization of noncash compensation                   --           3,149,334

Unrealized gain on marketable securities               --             145,250

Cumulative foreign currency translation
  adjustments                                          --             (27,108)

Net income for period                           9,764,547           9,764,547

Preferred stock dividends                      (1,867,877)         (1,867,877)
                                            -------------       -------------
Balance, June 30, 2000                      $(250,476,765)      $ 179,238,594
                                            =============       =============
</TABLE>



See notes to consolidated financial statements.



                                      (5)
<PAGE>   6

                        ALKERMES, INC. AND SUBSIDIARIES
                     CONSOLIDATED STATEMENTS OF CASH FLOWS
                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                              Three Months     Three Months
                                                                  Ended            Ended
                                                              June 30, 2000    June 30, 1999
                                                              -------------    -------------
<S>                                                           <C>              <C>
Cash flows from operating activities:
  Net income (loss).........................................   $ 9,764,547     $ (8,288,839)
  Adjustments to reconcile net income (loss) to net cash
     used by operating activities:
     Depreciation and amortization..........................     1,630,930        1,751,022
     Noncash interest expense...............................       116,116          209,380
     Compensation relating to issuance of common stock and
       grant of stock options and awards made...............     3,149,334           62,197
     Adjustments to other assets............................       261,646          258,939
     Changes in assets and liabilities:
       Receivables from collaborative arrangements..........   (27,417,230)         242,357
       Prepaid expenses and other current assets............    (1,578,488)        (161,428)
       Accounts payable and accrued expenses................     3,078,272       (1,367,768)
       Deferred revenues....................................      (200,035)      (2,531,779)
       Other long-term liabilities..........................       (19,898)         (19,897)
                                                               -----------     ------------
          Net cash used by operating activities.............   (11,214,806)      (9,845,816)
                                                               -----------     ------------
Cash flows from investing activities:
  Additions to property, plant and equipment, net...........    (1,311,452)      (1,413,373)
  Maturities (purchases) of short-term investments, net.....     9,348,594      (28,288,426)
  Maturities of long-term investments, net..................     5,970,206        3,283,308
  Increase in other assets..................................      (186,456)        (125,000)
                                                               -----------     ------------
          Net cash provided by (used by) investing
            activities......................................    13,820,892      (26,543,491)
                                                               -----------     ------------
Cash flows from financing activities:
  Proceeds from issuance of common stock, net...............       107,453          654,703
  Payment of preferred stock dividends......................    (1,867,877)      (2,098,714)
  Payment of long-term obligations..........................    (1,425,000)      (1,800,000)
  Proceeds from issuance of 1999 convertible exchangeable
     preferred stock........................................            --       35,000,000
                                                               -----------     ------------
          Net cash (used by) provided by financing
            activities......................................    (3,185,424)      31,755,989
                                                               -----------     ------------
Effect of exchange rate changes on cash.....................       (31,251)         (17,607)
                                                               -----------     ------------
Net decrease in cash and cash equivalents...................      (610,589)      (4,650,925)
Cash and cash equivalents, beginning of period..............     6,100,643        9,115,432
                                                               -----------     ------------
Cash and cash equivalents, end of period....................   $ 5,490,054     $  4,464,507
                                                               ===========     ============
Supplementary information:
  Cash paid for interest....................................   $   408,416     $    267,494
                                                               ===========     ============
</TABLE>

See notes to consolidated financial statements.


                                      (6)
<PAGE>   7
                         ALKERMES, INC. AND SUBSIDIARIES

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS


1.  BASIS OF PRESENTATION

The consolidated financial statements for the three month periods ended June 30,
2000 and 1999 are unaudited and include all adjustments which, in the opinion of
management, are necessary to present fairly the results of operations for the
periods then ended. All such adjustments are of a normal recurring nature. These
financial statements should be read in conjunction with the Company's Annual
Report on Form 10-K for the year ended March 31, 2000, which includes
consolidated financial statements and notes thereto for the years ended March
31, 2000, 1999 and 1998. In addition, the financial statements include the
accounts of Alkermes Controlled Therapeutics, Inc., Alkermes Controlled
Therapeutics Inc. II, Advanced Inhalation Research, Inc. ("AIR"), Alkermes
Investments, Inc., Alkermes Europe, Ltd. and Alkermes Development Corporation II
("ADC II"), wholly owned subsidiaries of the Company.

The results of the Company's operations for any interim period are not
necessarily indicative of the results of the Company's operations for any other
interim period or for a full fiscal year.

The preparation of the Company's financial statements in conformity with
generally accepted accounting principles necessarily 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 consolidated financial statements and the reported amounts of revenues and
expenses during the reporting period. Actual results could differ from those
estimates.

2.  COMPREHENSIVE INCOME (LOSS)

Comprehensive income is comprised of net income and other comprehensive income.
Other comprehensive income includes certain changes in equity of the Company
that are excluded from net income (loss). Specifically, other comprehensive
income includes unrealized holding gains and losses on the Company's
"available-for-sale" securities and changes in the cumulative foreign currency
translation adjustments.

Comprehensive income (loss) for the three months ended June 30, 2000 and 1999 is
as follows:
<TABLE>
<CAPTION>
                                                           Three Months          Three Months
                                                              Ended                 Ended
                                                          June 30, 2000         June 30, 1999
                                                          -------------         -------------
<S>                                                       <C>                  <C>
Net income (loss)                                           $ 9,764,547          $(8,288,839)
Cumulative foreign currency translation adjustments             (27,108)             (15,174)
Unrealized gain on marketable securities                        145,250              100,500
                                                            -----------          -----------
Comprehensive income (loss)                                 $ 9,882,689          $(8,203,513)
                                                            ===========          ===========
</TABLE>



                                      (7)
<PAGE>   8
The accumulated other comprehensive income is as follows:
<TABLE>

<S>                                                                    <C>
Balance March 31, 2000                                                  $6,742,064
Change for the three months ended June 30, 2000                            118,142
                                                                       -----------
Balance June 30, 2000                                                  $ 6,860,206
                                                                       ===========
</TABLE>

3.  EARNINGS PER SHARE

Basic net income (loss) per share is based on the weighted average number of
common shares outstanding. For the three months ended June 30, 2000, the
difference between basic and diluted shares used in the computation of earnings
per common share was 5,899,366 common equivalent shares. These securities
include options to purchase 5,516,734 shares of common stock and 382,632 shares
of common stock issuable upon conversion of non-voting common stock. Certain
securities have been excluded from the computation of diluted earnings per
common share for the three months ended June 30, 2000 because they would have an
antidilutive effect on earnings per common share. These securities include
7,760,251 shares of common stock issuable upon conversion of the convertible
exchangeable preferred stock and 2,952,030 shares of common stock for issuance
upon conversion of the 3-3/4% Convertible Subordinated Notes due 2007 (the
"3-3/4% Notes"). For the three months ended June 30, 1999, diluted net loss per
common share was the same as basic net loss per common share as the inclusion of
the weighted average number of shares of common stock issuable upon the exercise
of stock options, upon conversion of the convertible exchangeable preferred
stock and upon conversion of the 3-3/4% Notes would have been antidilutive.


                                      (8)
<PAGE>   9
ITEM 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
         RESULTS OF OPERATIONS

INTRODUCTION

Alkermes (together with our subsidiaries, "we" or "us") is developing innovative
pharmaceutical products based on sophisticated drug delivery systems. We have
several areas of focus: (i) controlled, sustained release of injectable drugs
lasting several days to several weeks, utilizing our ProLease(R) and Medisorb(R)
technologies; (ii) the development of pharmaceutical products based on
proprietary pulmonary drug delivery technologies utilizing our Advanced
Inhalation Research, Inc. ("AIR(TM)") technology; (iii) the delivery of drugs
into the brain past the blood-brain barrier utilizing our Cereport(R)
technology; and (iv) oral delivery of drugs utilizing our RingCap(TM) and dose
sipping technologies ("DST"). Since our inception in 1987, we have devoted
substantially all of our resources to research and development programs. We have
one product on the market, Nutropin Depot(TM), which was commercially launched
on June 28, 2000 by our collaborative partner Genentech, Inc. ("Genentech"). At
June 30, 2000, we had an accumulated deficit of approximately $250.5 million.
Alkermes does not expect to have net income in any future fiscal quarter for at
least the remainder of fiscal 2001.

We have funded our operations primarily through public offerings and private
placements of debt and equity securities, bank loans and payments under research
and development agreements with collaborators, including Alkermes Clinical
Partners, L.P. ("Clinical Partners"), a research and development limited
partnership whose operations commenced in April 1992 and whose funding ended
during June 1996. We generally develop our product candidates in collaboration
with others on whom we rely for funding, development, manufacturing and/or
marketing.

FORWARD-LOOKING STATEMENTS

Any statements set forth below or otherwise made in writing or orally by us with
regard to our expectations as to financial results and other aspects of our
business may constitute forward-looking statements within the meaning of the
Private Securities Litigation Reform Act of 1995. These statements relate to our
future plans, objectives, expectations and intentions and may be identified by
words like "believe," "expect," "may," "will," "should," "seek," or
"anticipate," and similar expressions.

Although we believe that our expectations are based on reasonable assumptions
within the bounds of our knowledge of our business and operations, our business
is subject to significant risks and there can be no assurance that actual
results of our development and manufacturing activities and our results of
operations will not differ materially from our expectations. Factors which could
cause actual results to differ from expectations include, among others: (i) we
may be unable to continue to manufacture our first product, Nutropin Depot, or
to manufacture future products on a commercial scale or economically; (ii)
Nutropin Depot may not produce significant revenues and, in commercial use, may
have unintended side effects, adverse reactions or incidents of misuse; (iii)
our collaborators could elect to terminate or delay programs at any time; (iv)
we and our collaborators may not be permitted by regulatory authorities to
undertake clinical trials for RingCap or DST or to undertake additional clinical
trials for ProLease, Cereport, Medisorb or AIR product candidates or clinical
trials


                                      (9)
<PAGE>   10
could be delayed; (v) our product candidates could be ineffective or unsafe
during clinical trials; (vi) even if clinical trials are completed and the data
is submitted to the Food and Drug Administration ("FDA") as a New Drug
Application ("NDA") for marketing approval and to other health authorities as a
marketing authorization application, the NDA or marketing authorization
application could fail to be accepted, or could fail to receive approval on a
timely basis, if at all; (vii) disputes with collaborators, termination of
collaborations or failure to negotiate acceptable new collaborative arrangements
for ProLease, Medisorb, AIR, RingCap or DST technologies, or for Cereport, could
occur; (viii) even if our product candidates appear promising at an early stage
of development, product candidates could fail to receive necessary regulatory
approvals, be difficult to manufacture on a large scale, be uneconomical, fail
to achieve market acceptance, be precluded from commercialization by proprietary
rights of third parties or experience substantial competition in the
marketplace; (ix) technological change in the biotechnology or pharmaceutical
industries could render our product candidates obsolete or noncompetitive; (x)
difficulties or set-backs in obtaining and enforcing our patents and
difficulties with the patent rights of others could occur; (xi) we could incur
difficulties or set-backs in obtaining the substantial additional funding
required to continue research and development programs and clinical trials; and
(xii) disputes with Clinical Partners over rights to Cereport and related
technology could occur.

RESULTS OF OPERATIONS

Net income for the three months ended June 30, 2000 was $9.8 million compared to
a net loss of $8.3 million for the same period in 1999. After taking into
account preferred stock dividends of $1.9 million for the three months ended
June 30, 2000, net income attributable to common shareholders was $7.9 million
or $0.15 basic earnings per common share and $0.13 diluted earnings per common
share. After taking into account preferred stock dividends of $2.1 million for
the three months ended June 30, 1999, net loss attributable to common
shareholders was $10.4 million or $0.21 basic and diluted loss per common share.
Net income for the quarter ended June 30, 2000 resulted from non-recurring
milestone revenues earned as a result of the June 28, 2000 launch of Nutropin
Depot by our collaborative partner, Genentech. Nutropin Depot is an injectable
long-acting formulation of Genentech's recombinant human growth hormone based on
our ProLease drug delivery system. Product revenues, cost of goods sold and
inventory related to Nutropin Depot have not been reported as the amounts were
immaterial to the consolidated financial statements. Alkermes does not expect to
have net income in any future fiscal quarter for at least the remainder of
fiscal 2001.

Our research and development revenue under collaborative arrangements for the
three months ended June 30, 2000 was $29.0 million compared to $5.8 million for
the corresponding period of the prior year. The increase was substantially the
result of non-recurring milestone revenues earned as a result of the launch of
Nutropin Depot. In addition, there was an increase in such revenue for the three
months ended June 30, 2000 as compared to the corresponding period of the prior
year as a result of increased funding earned under collaborative agreements
related to our ProLease, Medisorb and AIR technologies.

Total expenses were $22.4 million for the three months ended June 30, 2000 as
compared to $15.8 million for the three months ended June 30, 1999. The increase
for the three months ended June 30, 2000 as compared to the three months ended
June 30, 1999 is primarily related to an increase in noncash compensation
charges as well as an increase in research and development expenses, which are
discussed below.


                                      (10)
<PAGE>   11
Research and development expenses for the three months ended June 30, 2000 were
$14.4 million as compared to $12.3 million for the corresponding period of the
prior year. The increase in research and development expenses for the three
months ended June 30, 2000 as compared to the three months ended June 30, 1999
was mainly the result of an increase in salary and related benefits and other
costs associated with an increase in personnel as we advance our product
candidates through development and clinical trials and prepare for commercial
scale manufacturing. In addition, we had an increase in depreciation and
amortization expense as a result of additions to our manufacturing facilities.

General and administrative expenses for the three months ended June 30, 2000
were $4.8 million compared to $3.4 million for the corresponding period of the
prior year. The increase in the three months ended June 30, 2000 as compared to
the three months ended June 30, 1999 was primarily the result of increased
professional fees and information system costs. In addition there was an
increase in amortization expense related to offering costs incurred from the
sale of $200 million principal amount of our 3-3/4% Convertible Subordinated
Notes due 2007 (the "3-3/4% Notes") in February 2000.

Noncash compensation expense for the three months ended June 30, 2000 was $3.1
million as compared to $0.06 million for the corresponding period of the prior
year. Noncash compensation charges primarily relate to common stock issued and
stock options granted to certain employees, consultants and other individuals
associated with our subsidiary, AIR. Fluctuations in amounts are primarily a
result of changes in the market value of our common stock, partially offset by a
reduction in the number of shares of common stock subject to future vesting.

Interest income for the three months ended June 30, 2000 was $5.6 million
compared to $2.5 million for the corresponding period of the prior year. The
increase in such income for the three months ended June 30, 2000 as compared to
the corresponding period of the prior year was primarily the result of the
interest income earned on the increase in average cash and investment balances
mainly as a result of the investment of the proceeds from the sale of $200
million principal amount of the 3-3/4% Notes. Interest income also increased as
a result of an increase in interest rates as compared to the prior year period.

Interest expense for the three months ended June 30, 2000 was $2.4 million as
compared to $0.7 million for the corresponding period of the prior year. The
increase in the three months ended June 30, 2000 as compared to the three months
ended June 30, 1999 was primarily the result of interest costs related to the
3-3/4% Notes.

We do not believe that inflation and changing prices have had a material impact
on our results of operations.

LIQUIDITY AND CAPITAL RESOURCES

Cash and cash equivalents and short-term investments were approximately $327.4
million at June 30, 2000 as compared to $337.4 million at March 31, 2000. During
the three months ended June 30, 2000, the decrease in cash and cash equivalents
and short-term investments was primarily the result of cash used to fund
operations of the Company, to pay preferred stock dividends and to make
interest and principal payments on our indebtedness. The decrease was partially
offset by the increase in interest income earned on the invested proceeds from
the sale of the 3-3/4% Notes.

Receivables from collaborative arrangements include the non-recurring
milestone earned as a result of the June 28, 2000 launch of Nutropin Depot by
Genentech.

                                      (11)
<PAGE>   12
In addition, Investments include $12.5 million principal amount of high-grade
corporate notes and U.S. Government obligations with maturities ranging from 13
to 21 months. We invest in cash equivalents, U.S. Government obligations,
high-grade corporate notes and commercial paper. Our investment objectives for
all of our investments taken as a whole are, first, to assure conservation of
capital and liquidity, and second, to obtain investment income.

Our research and development costs to date have been financed primarily by sales
of debt and equity securities and payments under research and development
collaborative arrangements. We expect to incur significant additional research
and development and other costs, including costs related to preclinical studies,
clinical trials and facilities expansion. Therefore, we expect that our costs,
including research and development costs for all of our product candidates, will
exceed revenues significantly for at least the remainder of fiscal 2001, which
will result in losses from operations.

Capital expenditures were approximately $1.3 million for the three months ended
June 30, 2000, principally reflecting equipment purchases. Our capital
expenditures for equipment, facilities and building improvements have been
financed to date primarily with proceeds from bank loans and the sales of debt
and equity securities. Under the provisions of the existing loans, Fleet
National Bank has a security interest in certain of our assets.

We will continue to pursue opportunities to obtain additional financing in the
future. Such financing may be sought through various sources, including debt and
equity offerings, corporate collaborations, bank borrowings, lease arrangements
relating to fixed assets or other financing methods. The source, timing and
availability of any financings will depend on market conditions, interest rates
and other factors. Our future capital requirements will also depend on many
factors, including continued scientific progress in our research and development
programs, the magnitude of these programs, progress with preclinical testing and
clinical trials, the time and costs involved in obtaining regulatory approvals,
the costs involved in filing, prosecuting and enforcing patent claims, competing
technological and market developments, the establishment of additional
collaborative arrangements, the cost of manufacturing facilities and of
commercialization activities and arrangements and the cost of product
in-licensing and any possible acquisitions.

We may need to raise substantial additional funds for longer-term product
development, regulatory approvals and manufacturing or marketing activities that
we might undertake in the future. There can be no assurance that additional
funds will be available on favorable terms, if at all. If adequate funds are not
available, we may be required to curtail significantly one or more of our
research and development programs and/or obtain funds through arrangements with
collaborative partners or others that may require us to relinquish rights to
certain of our technologies, product candidates or future products.

ITEM 3.  QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

We own financial instruments that are sensitive to market risks as part of our
investment portfolio. The investment portfolio is used to preserve our capital
until it is required to fund operations, including our research and development
activities. Our Short-Term Investments and Investments consist of U.S.
Government obligations, high-grade corporate notes and commercial paper.
Substantially all investments mature within one year, are not callable by the
issuer and

                                      (12)
<PAGE>   13
have fixed interest rates. All of our Short-Term Investments and Investments are
currently held-to-maturity. These investments are subject to interest rate risk,
and could decline in value if interest rates fluctuate. Due to the conservative
nature of our Short-Term Investments and Investments, we do not believe that we
have a material exposure to interest rate risk.

Our "available-for-sale" marketable equity securities and the 3-3/4% Notes are
sensitive to changes in interest rates. Interest rate changes would result in a
change in the fair value of these financial instruments due to the difference
between the market interest rate and the rate at the date of purchase of the
financial instrument. A 10% decrease in year-end market interest rates would
result in no material impact on the net fair value of such interest-sensitive
financial instruments.

Our 3-3/4% Notes are sensitive to fluctuations in the price of our common stock
into which the 3-3/4% Notes are convertible. Changes in our common stock price
would result in changes in the fair value of the 3-3/4% Notes. Due to the
difference between the current market price and the market price at the date of
issuance of the 3-3/4% Notes, a 10% increase in the June 30, 2000 quarter-end
market price of the 3-3/4% Notes would result in an increase of approximately
$12.6 million on the net fair value of the 3-3/4% Notes.


                                      (13)
<PAGE>   14
PART II.  OTHER INFORMATION

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

At the Annual Meeting of Shareholders of the Company held on July 25, 2000, the
holders of Common Stock approved an amendment to the Stock Option Plan for
Non-Employee Directors to increase to 500,000 the number of shares issuable upon
the exercise of options granted thereunder, an increase of 200,000 shares, and
to increase the annual automatic grant to each non-employee director thereunder
to 20,000 shares, an increase of 15,000 shares. There were 32,044,894 votes for,
and 13,057,615 votes against, the amendment of the plan, no broker non-votes and
121,736 abstentions.

Also at the Annual Meeting of Shareholders, the holders of Common Stock approved
an amendment to the 1999 Stock Option Plan to increase to 7,400,000 the number
of shares issuable upon exercise of options granted thereunder, an increase of
2,400,000 shares. There were 32,745,528 votes for, and 12,353,378 votes against,
the amendment of the plan, no broker non-votes and 125,339 abstentions.

Also at the Annual Meeting of Shareholders, the holders of Common Stock elected
the following as directors for terms of one year expiring on the date of the
2001 Annual Meeting or until their respective successors are duly elected and
shall qualify:
<TABLE>
<CAPTION>
                                    Votes                     Authority
Nominee                             For                       Withheld
-------                             ---                       --------
<S>                                 <C>                       <C>
Floyd E. Bloom                      44,465,690                758,555

Robert A. Breyer                    44,466,766                757,479

John K. Clarke                      44,668,238                556,007

Richard F. Pops                     44,465,484                758,761

Alexander Rich                      44,464,192                760,053

Paul Schimmel                       44,468,944                755,301

Michael A. Wall                     44,458,450                765,795
</TABLE>


                                      (14)
<PAGE>   15
ITEM 6.   EXHIBITS AND REPORTS ON FORM 8-K

               (a) Exhibits:
                      Number        Exhibit

                      3.1(a)        Second Amended and Restated Articles of
                                    Incorporation of Alkermes, Inc., effective
                                    July 23, 1991. (Incorporated by reference to
                                    Exhibit 4.1(a) to the Company's Report on
                                    Form 10-Q for the quarter ended June 30,
                                    1991).

                      3.1(b)        Statement of Change of Registered Office of
                                    Alkermes, Inc. effective July 23, 1991.
                                    (Incorporated by reference to Exhibit 4.1(b)
                                    to the Company's Report on Form 10-Q for the
                                    quarter ended June 30, 1991).

                      3.1(c)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on November
                                    1, 1991. (Incorporated by reference to
                                    Exhibit 4.1(c) to the Company's Report on
                                    Form 10-Q for the quarter ended September
                                    30, 1991).

                      3.1(d)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as amended, as
                                    filed with the Pennsylvania Secretary of
                                    State on February 12, 1993. (Incorporated by
                                    reference to Exhibit 4.1(d) to the Company's
                                    Report on Form 10-Q for the quarter ended
                                    December 31, 1992).

                      3.1(e)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on February
                                    26, 1998. (Incorporated by reference to
                                    Exhibit 4.6 to the Company's Registration
                                    Statement on Form S-3, as amended (File No.
                                    333-50157)).

                      3.1(f)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on April 12,
                                    1999 (Non-Voting Common Stock Terms).
                                    (Incorporated by reference to Exhibit 3.1(g)
                                    to the Company's Report on Form 10-K for the
                                    fiscal year ended March 31, 1999).

                      3.1(g)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on April 28,
                                    2000 (effecting 2-for-1 stock split and
                                    increase in authorized shares).
                                    (Incorporated by reference to Exhibit 3.1(g)
                                    to the Company's Report on Form 10-K for the
                                    year ended March 31, 2000).

                      3.1(h)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on

                                      (15)
<PAGE>   16
                                    June 27, 2000. (Incorporated by reference to
                                    Exhibit 3.1(h) to the Company's Report on
                                    Form 10-K for the year ended March 31,
                                    2000).


                      3.2           Amended and Restated By-Laws of Alkermes,
                                    Inc., effective as of June 2, 1999.
                                    (Incorporated by reference to Exhibit 3.2 to
                                    the Company's Report on Form 10-K for the
                                    year ended March 31, 1999).

                      4.1           Specimen of Common Stock Certificate of
                                    Alkermes, Inc. (Incorporated by reference to
                                    Exhibit 4 to the Company's Registration
                                    Statement on Form S-1, as amended (File No.
                                    33-40250)).

                      4.2           Specimen of Preferred Stock Certificate of
                                    Alkermes, Inc. (Incorporated by reference to
                                    Exhibit 4.1 to the Company's Registration
                                    Statement on Form S-3, as amended (File No.
                                    333-50157)).

                      4.3           Specimen of Non-Voting Common Stock
                                    Certificate of Alkermes, Inc. (Incorporated
                                    by reference to Exhibit 4.4 to the Company's
                                    Report on Form 10-K for the fiscal year
                                    ended March 31, 1999).

                      4.4           Indenture, dated as of March 1, 1998,
                                    between Alkermes, Inc. and State Street Bank
                                    and Trust Company, as Trustee. (Incorporated
                                    by reference to Exhibit 4.7 to the Company's
                                    Registration Statement on Form S-3, as
                                    amended (File No. 333-50157)).

                      4.5           Indenture, dated as of February 18, 2000,
                                    between Alkermes, Inc. and State Street
                                    Bank and Trust Company, as Trustee
                                    (Incorporated by reference to Exhibit 4.6
                                    to the Company's Registration Statement
                                    on Form S-3 (File No. 333-31354)).

                      27            Financial Data Schedule.

(b)    During the quarter ended June 30, 2000, the Company filed Reports on Form
       8-K dated April 28, 2000 and June 12, 2000, each reporting under Item 5.


                                      (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.



                                       ALKERMES, INC.
                                       (Registrant)



Date:  August 14, 2000                 By:    /s/  Richard F. Pops
                                            ------------------------------------
                                             Richard F. Pops
                                             Chief Executive Officer and
                                               Director
                                               (Principal Executive Officer)


Date:  August 14, 2000                 By:   /s/  James M. Frates
                                           -------------------------------------
                                             James M. Frates
                                             Vice President, Chief
                                             Financial Officer and Treasurer
                                               (Principal Financial and
                                                  Accounting Officer)



                                      (17)
<PAGE>   18
                                  EXHIBIT INDEX


                      Exhibit
                      Number        Description


                      3.1(a)        Second Amended and Restated Articles of
                                    Incorporation of Alkermes, Inc., effective
                                    July 23, 1991. (Incorporated by reference to
                                    Exhibit 4.1(a) to the Company's Report on
                                    Form 10-Q for the quarter ended June 30,
                                    1991).

                      3.1(b)        Statement of Change of Registered Office of
                                    Alkermes, Inc. effective July 23, 1991.
                                    (Incorporated by reference to Exhibit 4.1(b)
                                    to the Company's Report on Form 10-Q for the
                                    quarter ended June 30, 1991).

                      3.1(c)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on November
                                    1, 1991. (Incorporated by reference to
                                    Exhibit 4.1(c) to the Company's Report on
                                    Form 10-Q for the quarter ended September
                                    30, 1991).

                      3.1(d)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as amended, as
                                    filed with the Pennsylvania Secretary of
                                    State on February 12, 1993. (Incorporated by
                                    reference to Exhibit 4.1(d) to the Company's
                                    Report on Form 10-Q for the quarter ended
                                    December 31, 1992).

                      3.1(e)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on February
                                    26, 1998. (Incorporated by reference to
                                    Exhibit 4.6 to the Company's Registration
                                    Statement on Form S-3, as amended (File No.
                                    333-50157)).

                      3.1(f)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on April 12,
                                    1999 (Non-Voting Common Stock Terms).
                                    (Incorporated by reference to Exhibit 3.1(g)
                                    to the Company's Report on Form 10-K for the
                                    fiscal year ended March 31, 1999).

                      3.1(g)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on April 28,
                                    2000 (effecting 2-for-1 stock split and
                                    increase in authorized shares).
                                    (Incorporated by reference to Exhibit 3.1(g)
                                    to the Company's Report on Form 10-K for the
                                    year ended March 31, 2000).


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<PAGE>   19
                      3.1(h)        Amendment to the Second Amended and Restated
                                    Articles of Incorporation, as filed with the
                                    Pennsylvania Secretary of State on June 27,
                                    2000. (Incorporated by reference to Exhibit
                                    3.1(h) to the Company's Report on Form 10-K
                                    for the year ended March 31, 2000).

                      3.2           Amended and Restated By-Laws of Alkermes,
                                    Inc., effective as of June 2, 1999.
                                    (Incorporated by reference to Exhibit 3.2 to
                                    the Company's Report on Form 10-K for the
                                    year ended March 31, 1999).

                      4.1           Specimen of Common Stock Certificate of
                                    Alkermes, Inc. (Incorporated by reference to
                                    Exhibit 4 to the Company's Registration
                                    Statement on Form S-1, as amended (File No.
                                    33-40250)).

                      4.2           Specimen of Preferred Stock Certificate of
                                    Alkermes, Inc. (Incorporated by reference to
                                    Exhibit 4.1 to the Company's Registration
                                    Statement on Form S-3, as amended (File No.
                                    333-50157)).

                      4.3           Specimen of Non-Voting Common Stock
                                    Certificate of Alkermes, Inc. (Incorporated
                                    by reference to Exhibit 4.4 to the Company's
                                    Report on Form 10-K for the fiscal year
                                    ended March 31, 1999).

                      4.4           Indenture, dated as of March 1, 1998,
                                    between Alkermes, Inc. and State Street Bank
                                    and Trust Company, as Trustee. (Incorporated
                                    by reference to Exhibit 4.7 to the Company's
                                    Registration Statement on Form S-3, as
                                    amended (File No. 333-50157)).

                      4.5           Indenture, dated as of February 18, 2000,
                                    between Alkermes, Inc. and State Street
                                    Bank and Trust Company, as Trustee
                                    (Incorporated by reference to Exhibit 4.6
                                    to the Company's Registration Statement
                                    on Form S-3 (File No. 333-31354)).

                      27            Financial Data Schedule.



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