<PAGE>   1
                       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 September 30, 1998

[ ]      QUARTERLY 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.


                                 INDEX



                                                                        Page No.
                                                                        --------
PART I - FINANCIAL INFORMATION

           Item 1.  Financial Statements

                    Balance Sheets                                          3
                    -September 30, 1998 and December 31, 1997

                    Statements of Operations                                4
                    -Three months ended September 30, 1998 and 1997 
                    -Nine months ended September 30, 1998 and 1997

                    Statements of Cash Flows                                5
                    -Nine months ended September 30, 1998 and 1997

                    Notes to Financial Statements                           6

           Item 2.  Management's Discussion and Analysis of                 7
                    Financial Condition and Results of Operations

PART II - OTHER INFORMATION

           Item 6.  Exhibits, Financial Statement Schedules and Reports    10
                    on Form 8-K

SIGNATURES                                                                 11

EXHIBIT INDEX                                                              12



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ITEM 1.  FINANCIAL STATEMENTS:

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

                                 BALANCE SHEETS
                                   (Unaudited)
<TABLE>
<CAPTION>
                                                   September 30,       December 31,
                                                       1998                1997
                                                   ------------        ------------
<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    Nine Months     Nine Months
                                               Ended           Ended           Ended          Ended
                                            September 30,   September 30,   September 30,  September 30,
                                                1998            1997            1998           1997
                                            -------------   -------------   -------------  -------------
<S>                                         <C>             <C>             <C>            <C>
Revenue:
    Interest income                            $ --           $    15           $--          $   232
                                               ----           -------           ---          -------

Expenses:
    General and administrative                   --             2,425            --            4,764
                                               ----           -------           ---          -------
                                                 --             2,425            --            4,764
                                               ----           -------           ---          -------

Net loss                                       $ --           $(2,410)          $--          $(4,532)
                                               ====           =======           ===          =======

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

Average Units Outstanding                       921               921           921              921
                                               ====           =======           ===          =======
</TABLE>


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

                              STATEMENTS OF CASH FLOWS
                                    (Unaudited)

<TABLE>
<CAPTION>
                                                                Nine Months     Nine Months         
                                                                   Ended           Ended            
                                                                September 30,   September 30,       
                                                                   1998             1997            
                                                                -------------   -------------
<S>                                                             <C>            <C>                 
Cash flows from operating activities:                                                               
   Net loss                                                         $--        $ (4,532)            
   Adjustment to reconcile net loss to net cash used for                                            
        operating activities:                                                                       
        Changes in assets and liabilities:                                                          
             Accrued expenses                                        --         (28,272)            
                                                                    ---        --------             
                                                                                                    
                  Net cash used for operating activities             --         (32,804)            
                                                                    ---        --------             
                                                                                                    
Net decrease in cash and cash equivalents                            --         (32,804)            
                                                                                                    
Cash and cash equivalents, beginning of period                       --          32,804             
                                                                                                    
                                                                    ===        ========             
Cash and cash equivalents, end of period                            $--        $     --             
                                                                    ===        ========             
</TABLE>


See notes to financial statements.



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                        ALKERMES CLINICAL PARTNERS, L.P.
                                        
                         NOTES TO FINANCIAL STATEMENTS

1.  BASIS OF PRESENTATION

The financial statements for Alkermes Clinical Partners, L.P. (the
"Partnership") for the three and nine month periods ended September 30, 1998 and
1997, 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, 1997, which includes
financial statements and notes thereto for the years ended December 31, 1997,
1996 and 1995.

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 the General Partner. There were no losses attributable to
the General Partner or the Limited Partners for the three and nine months ended
September 30, 1998. The entire net loss for the three and nine months ended
September 30, 1997, was attributable to the General Partner, and consequently,
there were no losses attributable to the Limited Partners for such periods. In
February 1997, the Financial Accounting Standards Board released Statement of
Financial Accounting Standards No. 128 ("SFAS No. 128"), "Earnings per Share,"
which the Partnership adopted in the fourth quarter of 1997. The adoption of
SFAS No. 128 did not have any impact on the Partnership's financial statements
because the Partnership does not have, and is not expected to have, any common
stock equivalents.

3.  COMPLETION OF SCHEDULED FUNDING

For the three and nine months ended September 30, 1998, 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(TM), formerly known as RMP-7(TM), 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.

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 September 30, 1998, the Partnership is expected to have no future
liquidity or capital resources requirements other than those funded by Alkermes.


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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. Although the General Partner believes that its
expectations are based on reasonable assumptions within the bounds of its
knowledge of its business and operations, the Partnership's and the Company's
businesses are subject to significant risks and there can be no assurance that
actual results of the Partnership's or the Company's development activities and
their respective results of operations will not differ materially from
expectations. Accordingly, the Partnership hereby identifies the following
important factors, among others, which could cause its results to differ from
any results which might be projected, forecasted or estimated by the Partnership
or the General Partner in any such forward-looking statements: (i) the
Partnership and the Company could not be permitted by regulatory authorities to
undertake additional clinical trials for Cereport(TM) (formerly known as
RMP-7(TM)) or clinical trials could be delayed or regulatory authorities could
require additional clinical trials; (ii) Cereport could be ineffective or unsafe
during clinical trials; (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) even if Cereport appears
promising at its current 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 (v) technological change in the
biotechnology or pharmaceutical industries could render Cereport obsolete or
noncompetitive.

RESULTS OF OPERATIONS

Revenues

The Partnership's sole source of revenue for the three and nine months ended
September 30, 1997 was the interest earned on the investments made with the
capital contributions made by the General Partner and the limited partners of
the Partnership (the "Limited Partners") prior to their disbursement to Alkermes
for research and development and/or other Partnership expenses. There was no
interest income for the three and nine months ended September 30, 1998, as
compared to $15 and $232 for the corresponding periods of the prior year.
Interest income for the three and nine months ended September 30, 1998 as
compared to the same period in 1997 decreased as a result of the depletion of
the Partnership's cash. The Partnership anticipates that it will have no
interest income in the foreseeable future as the Partnership's assets were
depleted during the quarter ended September 30, 1997. The decrease in the cash
of the Partnership is a result of the completion of the payment of the
development funding to Alkermes during the quarter ended June 30, 1996. The
development funding to Alkermes was made pursuant to the product development
agreement between Alkermes and the Partnership (the "Product Development
Agreement").




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<PAGE>   8


Expenses

There were no research and development expenses for the three and nine months
ended September 30, 1998 and 1997 as a result of the completion of the
development funding to Alkermes pursuant to the Product Development Agreement.

There were no general and administrative expenses for the three and nine months
ended September 30, 1998, as compared to $2,425 and $4,764 for the three and
nine months ended September 30, 1997. The decrease was the result of the
depletion of the Partnership's assets during the quarter ended September 30,
1997. 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 (see Liquidity and Capital Resources).

LIQUIDITY AND CAPITAL RESOURCES

At September 30, 1998, the Partnership had no remaining current assets or
current 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(TM)
from capital contributions received from Partners. Such development is being
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.

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.

The Partnership does not own or use any software systems or any other automated
equipment. Alkermes and the companies with which it does business, however, use
software systems and embedded technology in the conduct of their operations.
Many software systems and much technology in use today are unable to distinguish
the year 2000 and the year 1900 because they use a two-digit shorthand for
calendar dates. If Alkermes does not identify and correct any such shorthand
prior to January 1, 2000, its operations could be disrupted. Alkermes'
operations could 

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<PAGE>   9

also be disrupted if the companies with which Alkermes does significant business
similarly are not year 2000 compliant, and such failure adversely affects their
ability to do business with Alkermes.

To address these issues, Alkermes has undertaken a three-step comprehensive
project. The first step is to identify all of its software and embedded
technology. The second step is to determine whether any of Alkermes' software
and technology use the two-digit shorthand and to determine whether the
companies with which Alkermes does significant business will be year 2000
compliant. The third step is to correct or replace all such software and
technology and then to test the corrected or replacement software and
technology. Alkermes has completed the first step of the project, expects to
complete the second step by the end of calendar year 1998 and will commence the
third step promptly upon completion of the second step. Upon the completion of
the second step, the Company will assess the need for a contingency plan. This
project is being conducted by Alkermes primarily using internal resources.
Alkermes cannot estimate the cost of completion of the project or establish any
contingency plan until it completes the second step, and there can be no
assurance that the cost of completion of the project will not be material, that
the project will be completed on a timely basis, that any contingency plans
could be promptly developed and implemented or that the use of its internal
resources to complete the project will not adversely affect other aspects of its
business. In the event that any of the companies with which Alkermes does
significant business do not successfully achieve year 2000 compliance on a
timely basis, Alkermes' business could be adversely affected.

After September 30, 1998, the Partnership is expected to have no future
liquidity or capital resources requirements other than those funded by Alkermes.


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

         (a) Exhibits:
                     Number                     Exhibit
                     ------                     -------
                     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.*

                     11          Statement Regarding Computation of Per
                                 Share Loss.

                     27          Financial Data Schedule.

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

         (b) The Registrant has not filed any reports on Form 8-K during the
             quarter ended September 30, 1998.


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<PAGE>   11



                                   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:  November 13, 1998            By:   /s/ Richard F. Pops
                                        ----------------------------------
                                        Richard F. Pops
                                        Director, President and Chief Executive
                                        Officer (Principal Executive Officer)

Date:  November 13, 1998            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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                                  EXHIBIT INDEX

                     Exhibit
                     Number      Description
                     -------     -----------
                     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.*

                     11          Statement Regarding Computation of Per
                                 Share Loss.

                     27          Financial Data Schedule.

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



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