<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 March 31, 2001

     [ ]  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 0-26758

                        ALKERMES CLINICAL PARTNERS, L.P.
             ------------------------------------------------------
             (Exact name of registrant as specified in its charter)

            DELAWARE                                              043-145043
-------------------------------                              -------------------
(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 ___


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                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)

                                      INDEX


<TABLE>
<CAPTION>
                                                                             Page No.
                                                                             --------

<S>                                                                          <C>
PART I - FINANCIAL INFORMATION

          Item 1.   Financial Statements

                    Balance Sheets                                               3
                    -March 31, 2001 and December 31, 2000

                    Statements of Operations                                     4
                    -Three months ended March 31, 2001 and 2000

                    Statements of Cash Flows                                     5
                    -Three months ended March 31, 2001 and 2000

                    Notes to Financial Statements                                6

          Item 2.   Management's Discussion and Analysis of                      8
                    Financial Condition and Results of Operations

PART II - OTHER INFORMATION

          Item 6.   Exhibits, Financial Statement Schedules and Reports         11
                    on Form 8-K

SIGNATURES                                                                      12

EXHIBIT INDEX                                                                   13
</TABLE>


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<PAGE>   3


ITEM 1. FINANCIAL STATEMENTS:

                        ALKERMES CLINICAL PARTNERS, L.P.
                            (A LIMITED PARTNERSHIP)

                                 BALANCE SHEETS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                                                March 31,    December 31,
                                                                  2001           2000
                                                                ---------    ------------

<S>                                                             <C>          <C>
                                     ASSETS

Total Assets                                                       $ --          $ --
                                                                   ====          ====


                        LIABILITIES AND PARTNERS' CAPITAL


Total Liabilities and Partners' Capital                            $ --          $ --
                                                                   ====          ====
</TABLE>


See notes to financial statements.


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<PAGE>   4


                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)

                            STATEMENTS OF OPERATIONS
                                   (Unaudited)


<TABLE>
<CAPTION>
                                               Three Months      Three Months
                                                   Ended             Ended
                                                 March 31,         March 31,
                                                   2001              2000
                                               ------------      ------------

<S>                                            <C>               <C>
Revenue:                                         $    --           $    --
                                                 -------           -------

Expenses:
    General and administrative                     2,043             7,754
                                                 -------           -------
                                                   2,043             7,754
                                                 -------           -------

Net loss                                         $(2,043)          $(7,754)
                                                 =======           =======

Net Loss Per Class A and B Unit                  $    --           $    --
                                                 =======           =======

Average Class A and B Units Outstanding              921               921
                                                 =======           =======
</TABLE>


See notes to financial statements.


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<PAGE>   5


                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)

                            STATEMENTS OF CASH FLOWS
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                                   Three Months       Three Months
                                                                      Ended              Ended
                                                                    March 31,          March 31,
                                                                       2001               2000
                                                                   ------------       ------------

<S>                                                                <C>                <C>
Cash flows from operating activities:
    Net loss                                                          $(2,043)          $(7,754)

                                                                      -------           -------
                   Net cash used by operating activities               (2,043)           (7,754)
                                                                      -------           -------

Cash flows from financing activities:
    General Partner's capital contributions                             2,043             7,754
                                                                      -------           -------
                   Net cash provided by financing activities            2,043             7,754
                                                                      -------           -------

Net decrease in cash                                                       --                --

Cash, beginning of period                                                  --                --

                                                                      -------           -------
Cash, end of period                                                   $    --           $    --
                                                                      =======           =======
</TABLE>


See notes to financial statements.


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<PAGE>   6


                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)

                          NOTES TO FINANCIAL STATEMENTS

1. BASIS OF PRESENTATION

The financial statements for Alkermes Clinical Partners, L.P. (the
"Partnership") for the three month periods ended March 31, 2001 and 2000, 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 Partnership's Annual Report on
Form 10-K for the year ended December 31, 2000, which includes financial
statements and notes thereto for the years ended December 31, 2000, 1999 and
1998.

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

2. NET LOSS PER CLASS A AND B LIMITED PARTNERSHIP INTEREST

Net loss per Class A and B limited partnership interest is calculated with the
net loss attributable only to the limited partners of the Partnership (each, a
"Limited Partner" and collectively, the "Limited Partners") and excludes the
loss attributable to Alkermes Development Corporation II (the "General
Partner"). There were no losses attributable to the Limited Partners for the
three months ended March 31, 2001 and 2000.

3. COMPLETION OF SCHEDULED FUNDING

For the three months ended March 31, 2001 and 2000, the Partnership incurred no
research and development expenses related to the RMP(TM) program,
notwithstanding the continuing development of such product candidate. The
Partnership was providing funding to Alkermes, Inc. ("Alkermes") for research
and development expenses for Cereport(R) from capital contributions received
from Partners. Funding to Alkermes ended during the quarter ended June 30, 1996
when such capital contributions were substantially depleted. None of the
Partners of the Partnership is obligated to make any further capital
contributions. Since the funding was not sufficient for Alkermes to complete
clinical trials and seek regulatory approval of Cereport, Alkermes has used its
own resources, and intends to continue to use its own resources, to develop
Cereport. Alkermes has obtained and intends to continue to obtain such resources
through equity offerings, bank borrowings and its collaborative arrangements.
Alkermes is required to fund the development of Cereport to maintain its
Purchase Option with the Limited Partners.


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<PAGE>   7


Alkermes is also obligated, through the General Partner, to perform
administrative services for the Partnership, such as preparing financial
statements, tax returns and reports to Partners. Alkermes intends to continue to
cause the General Partner to perform such services at its expense since the
Partnership's current assets are depleted, unless it exercises its Purchase
Option and thereby acquires all the interests in the Partnership. The services
performed by Alkermes and the General Partner constitute all of the activities
undertaken by or on behalf of the Partnership.

After March 31, 2001, the Partnership is expected to have no future liquidity or
capital resources requirements other than those funded by Alkermes.


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<PAGE>   8


ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS


INTRODUCTION

Alkermes Clinical Partners, L.P. (the "Partnership") was formed on February 7,
1992, and is managed by its general partner, Alkermes Development Corporation II
(the "General Partner"), a wholly owned subsidiary of Alkermes, Inc. ("Alkermes"
or the "Company"). The Partnership was organized to fund the further development
and clinical testing of a family of molecules, designated by Alkermes as
Receptor-Mediated Permeabilizers(TM) ("RMPs(TM)"), for human pharmaceutical use
in the United States and Canada.

IMPORTANT FACTORS REGARDING FORWARD-LOOKING STATEMENTS

Any statements set forth below or otherwise made in writing or orally by the
Partnership or the General Partner with regard to its expectations as to
financial results and other aspects of its business may constitute
forward-looking statements within the meaning of the Private Securities
Litigation Reform Act of 1995. These statements can be identified by
forward-looking words such as "may", "will", "expects", "anticipates",
"believes", "estimates", "continues" or similar words. Although the General
Partner believes that its expectations are based on reasonable assumptions
within the bounds of its knowledge of its business and operations, there can be
no assurance that actual results of the Partnership's or the Company's
development activities and the Partnership's results of operations will not
differ materially from its expectations. Factors which could cause actual
results to differ from expectations include, among others:

(i)   the Partnership and the Company could not be permitted by regulatory
      authorities to undertake additional clinical trials for Cereport(R) or
      clinical trials could be delayed or regulatory authorities could require
      additional clinical trials before approving Cereport;
(ii)  clinical trials for Cereport may not proceed as planned, the trials may
      require more time to enroll patients than anticipated, and even if they
      are completed Cereport could prove to be ineffective or unsafe;
(iii) the Company could incur difficulties or set-backs in obtaining the
      substantial additional funding required to continue research and
      development programs and clinical trials;
(iv)  the Company could reduce or discontinue funding of Cereport;
(v)   even if Cereport appears promising at an early stage of development, it
      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;
      and
(vi)  technological change in the biotechnology or pharmaceutical industries and
      the approval of other drugs or therapies to treat brain tumors could
      render Cereport obsolete or noncompetitive.


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<PAGE>   9


RESULTS OF OPERATIONS

Revenues

The Partnership had no revenue for the three months ended March 31, 2001 and
2000. The Partnership anticipates that it will have no revenues in the
foreseeable future.

Expenses

The Partnership had no research and development expenses for the three months
ended March 31, 2001 and 2000. The research and development expenses were zero
because of the completion of the development funding to Alkermes pursuant to the
product development agreement between Alkermes and the Partnership (the "Product
Development Agreement").

General and administrative expenses for the three months ended March 31, 2001
were $2,043 as compared to $7,754 for the three months ended March 31, 2000. The
decrease for the three months ended March 31, 2001 compared to March 31, 2000
was mainly a result of decreased professional service fees. Alkermes is
obligated through the General Partner to perform general and administrative
services for the Partnership at its expense, unless Alkermes exercises its
Purchase Option and thereby acquires all limited partnership interests in the
Partnership (see Liquidity and Capital Resources).

LIQUIDITY AND CAPITAL RESOURCES

At March 31, 2001, the Partnership had no remaining assets or liabilities.

The Partnership's primary source of funding and capital resources had been the
annual capital contributions by the Limited Partners and the General Partner.
The Limited Partners' capital contributions were remitted to the Partnership in
four annual installments, the fourth and final payment of which was due on April
15, 1995. There have been and will be no additional capital contributions
received by the Partnership from the Limited Partners after the quarter ended
June 30, 1996.

The Partnership was funding research and development expenses for Cereport from
capital contributions received from Partners. Such development was and continues
to be conducted for the Partnership by Alkermes pursuant to the Product
Development Agreement. The research and development funding to Alkermes ended
during the quarter ended June 30, 1996 when such capital contributions were
substantially depleted. None of the Partners is obligated to make any further
capital contributions. Because the funding was not sufficient for Alkermes to
complete clinical trials and seek regulatory approval of Cereport, Alkermes has
used its own resources, and intends to continue to obtain such resources through
equity offerings, bank borrowings and its collaborative arrangements. Effective
September 30, 1997, Alkermes entered into an agreement with ALZA Corporation
related to the development and commercialization of Cereport. Alkermes is
required to fund the development of Cereport to maintain its Purchase Option
with the Limited Partners.


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<PAGE>   10


The Partnership used its remaining cash and cash equivalents during the quarter
ended September 30, 1997 to pay for administrative services for the Partnership.
Alkermes is obligated, through the General Partner, to perform administrative
services for the Partnership, such as preparing financial statements, tax
returns and reports to the Limited Partners. Alkermes intends to continue to
cause the General Partner to perform such services at its expense since the
Partnership's current assets are depleted to maintain its Purchase Option with
the Limited Partners, unless it exercises its Purchase Option and thereby
acquires all limited partnership interests in the Partnership. The activities
performed by Alkermes and the General Partner constitute all of the activities
undertaken by or on behalf of the Partnership.

After March 31, 2001, the Partnership is expected to have no future liquidity or
capital resources requirements other than those funded by Alkermes.


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<PAGE>   11


ITEM 6. EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K

        (a) Exhibits:
<TABLE>
<CAPTION>
                     Number                            Exhibit
                     ------                            -------

<S>                                <C>
                      3.1          Alkermes Clinical Partners, L.P. Agreement of Limited
                                   Partnership, dated as of February 7, 1992.*

                      3.1(a)       Amendment No. 1 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of
                                   September 29, 1992.*

                      3.1(b)       Amendment No. 2 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of
                                   March 30, 1993.*

                      4.1          Alkermes Clinical Partners, L.P. Agreement of Limited
                                   Partnership, dated as of February 7, 1992.*

                      4.1(a)       Amendment No. 1 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of
                                   September 29, 1992.*

                      4.1(b)       Amendment No. 2 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of March
                                   30, 1993.*
</TABLE>

*    Incorporated by reference to Exhibits to the Registrant's Registration
     Statement on Form 10 filed September 13, 1995.

          (b)  Since the beginning of the quarter ended March 31, 2001 the
               Registrant has not filed any reports on Form 8-K.


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<PAGE>   12


                                   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 CLINICAL PARTNERS, L.P.
                                        (Registrant)

                                        By its General Partner

                                        ALKERMES DEVELOPMENT CORPORATION II


Date: May 15, 2001                      By: /s/ Richard F. Pops
                                            ------------------------------------
                                            Richard F. Pops
                                            Director, President and Chief
                                            Executive Officer (Principal
                                            Executive Officer)


Date: May 15, 2001                      By: /s/ James M. Frates
                                            ------------------------------------
                                            James M. Frates
                                            Director, Vice President, Chief
                                            Financial Officer, Treasurer and
                                            Assistant Secretary (Principal
                                            Financial and Accounting Officer)


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<PAGE>   13


                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
                     Number                            Exhibit
                     ------                            -------

<S>                                <C>
                      3.1          Alkermes Clinical Partners, L.P. Agreement of Limited
                                   Partnership, dated as of February 7, 1992.*

                      3.1(a)       Amendment No. 1 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of
                                   September 29, 1992.*

                      3.1(b)       Amendment No. 2 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of
                                   March 30, 1993.*

                      4.1          Alkermes Clinical Partners, L.P. Agreement of Limited
                                   Partnership, dated as of February 7, 1992.*

                      4.1(a)       Amendment No. 1 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of
                                   September 29, 1992.*

                      4.1(b)       Amendment No. 2 to Alkermes Clinical Partners, L.P.
                                   Agreement of Limited Partnership, dated as of March
                                   30, 1993.*
</TABLE>

*    Incorporated by reference to Exhibits to the Registrant's Registration
     Statement on Form 10 filed September 13, 1995.


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