<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, 1996

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

            For the transaction 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
                                              ---    --- 

<PAGE>   2
                        ALKERMES CLINICAL PARTNERS, L.P.


                                      INDEX
                                      -----

                                                                        Page No.
                                                                        --------

PART I - FINANCIAL INFORMATION

          Item 1. Financial Statements

                  Balance Sheets                                            3
                  -September 30, 1996 and December 31, 1995
 
                  Statements of Operations                                  4
                  -Three months ended September 30, 1996 and 1995
                  -Nine months ended September 30, 1996 and 1995

                  Statements of Cash Flows                                  5
                  -Nine months ended September 30, 1996 and 1995

                  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               9
                  Reports on Form 8-K                                       
                  

SIGNATURES                                                                 10

EXHIBIT INDEX                                                              11


                                      (2)
<PAGE>   3
ITEM 1. FINANCIAL STATEMENTS:

                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)
<TABLE> 
                                                 BALANCE SHEETS
                                                  (Unaudited)
<CAPTION>  
                                                                                  September 30,     December 31,
                                                                                      1996              1995
                                                                                  -------------     ------------
                                                  A S S E T S                                             
<S>                                                                                  <C>             <C>        
Current Assets:                                                                      
      Cash and cash equivalents                                                      $40,518         $2,365,478
      Prepaid expenses to Alkermes, Inc.                                                  --            500,000
      Interest receivable                                                                 --              1,375
                                                                                     -------         ----------
           Total current assets                                                       40,518          2,866,853
                                                                                                    
Other Assets:                                                                                       
      Organization costs, less amortization of $221,112 and $205,726                      --             15,386
                                                                                     -------         ----------
                                                                                                    
Total Assets                                                                         $40,518         $2,882,239
                                                                                     =======         ==========
                                                                                                    
                                                                                                    
                         L I A B I L I T I E S  A N D  P A R T N E R S'  C A P I T A L                   
                                                                                                    
Current Liabilities:                                                                                
      Accrued expenses                                                               $14,998         $   26,464
                                                                                     -------         ----------
           Total current liabilities                                                  14,998             26,464
                                                                                     -------         ----------
                                                                                                    
Partners' capital                                                                     25,520          2,859,147
Less:  Notes receivable from limited partners                                             --             (3,372)
                                                                                     -------         ----------
                                                                                      25,520          2,855,775
                                                                                     -------         ----------
                                                                                                    
Total Liabilities and Partners' Capital                                              $40,518         $2,882,239
                                                                                     =======         ==========
</TABLE>

See notes to financial statements.

                                     (3)

<PAGE>   4

                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)
<TABLE>
                                                  STATEMENTS OF OPERATIONS
                                                        (Unaudited)
<CAPTION>

                                      Three Months    Three Months        Nine Months        Nine Months
                                          Ended           Ended              Ended              Ended
                                      September 30,   September 30,      September 30,      September 30,
                                          1996            1995               1996               1995
                                      -------------   -------------      -------------      -------------
<S>                                      <C>           <C>                <C>                <C>
Revenue:                                                    
     Interest income                     $   329       $    90,832        $    11,287        $   236,564
                                         -------       -----------        -----------        -----------
Expenses:                                                   
     Research and development                 --         2,698,000          4,850,000          8,284,000
     General and administrative            8,136            41,369             49,815            102,153
     Interest expense                         --                --                 --             98,666
                                         -------       -----------        -----------        -----------
                                           8,136         2,739,369          4,899,815          8,484,819
                                         -------       -----------        -----------        -----------
                                                            
Net loss                                 $(7,807)      $(2,648,537)       $(4,888,528)       $(8,248,255)
                                         =======       ===========        ===========        ===========
                                                            
Net Loss Per Class A and B                                  
     Limited Partnership Interest        $    (8)      $    (2,847)       $    (5,255)       $    (8,866)
                                         =======       ===========        ===========        ===========
                                                            
Average Limited Partnership                                 
     Interests Outstanding                   921               921                921                921
                                         =======       ===========        ===========        ===========
                                                            
</TABLE>            

See notes to financial statements.

                                     (4)

<PAGE>   5
                        ALKERMES CLINICAL PARTNERS, L.P.
                             (A LIMITED PARTNERSHIP)
<TABLE>
                                 STATEMENTS OF CASH FLOWS
                                       (Unaudited)
<CAPTION>
                                                               Nine Months      Nine Months
                                                                  Ended            Ended
                                                              September 30,    September 30,
                                                                  1996             1995
                                                              -------------    -------------
<S>                                                            <C>              <C>
Cash flows from operating activities:
   Net loss                                                    $(4,888,528)     $(8,248,255)
   Adjustment to reconcile net loss to net cash used for
      operating activities:
      Amortization                                                  15,386           41,459
      Changes in assets and liabilities:
         Prepaid expenses to Alkermes, Inc.                        500,000        1,884,000
         Interest receivable                                         1,375           24,320
         Accrued expenses                                          (11,466)          26,423
         Accrued interest payable                                       --         (256,459)
         
                                                               -----------      -----------
                  Net cash used by operating activities         (4,383,233)      (6,528,512)
                                                               -----------      -----------

Cash flows from investing activities:
   Purchases of short-term investments                                  --       (2,698,191)
                                                               -----------      -----------

Cash flows from financing activities:
   Payment of note payable to Alkermes, Inc.                            --       (4,735,000)
   Partners' cash capital contributions                          2,058,273       10,755,238
                                                               -----------      -----------

                  Net cash provided by financing activities      2,058,273        6,020,238
                                                               -----------      -----------

Net decrease in cash and cash equivalents                       (2,324,960)      (3,206,465)

Cash and cash equivalents, beginning of period                   2,365,478        3,308,800

                                                               -----------      -----------
Cash and cash equivalents, end of period                       $    40,518      $   102,335
                                                               ===========      ===========

Noncash Supplemental Disclosure -
   Write-off of notes receivable from limited partners         $        --      $   184,788
                                                               ===========      ===========
</TABLE>  
See notes to financial statements.

                                      (5)

<PAGE>   6
                        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, 1996 and
1995, 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, 1995, which includes
financial statements and notes thereto for the years ended December 31, 1995,
1994 and 1993.

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. PRODUCT DEVELOPMENT AGREEMENT
   -----------------------------

Alkermes, Inc. has been issued U.S. Patent No. 5,506,206 in April 1996. The
patent covers the specific chemical composition of RMP-7[Trademark] and the 
rights to the patent have been licensed to the Partnership pursuant to a 
product development agreement.

3. ACCRUED EXPENSES
   ----------------

Included in accrued expenses at September 30, 1996 are amounts totaling
approximately $3,500 which are due to Alkermes, Inc.

                                     (6)

<PAGE>   7


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 Alkermes Development Corporation, II (the "General
Partner"), a wholly owned subsidiary of Alkermes, Inc. ("Alkermes"). The
Partnership was organized to fund the further development and clinical testing
of a family of molecules, designated by Alkermes as Receptor-Mediated
Permeabilizers[Trademark] ("RMPs[Trademark]"), for human pharmaceutical use in
the United States and Canada.

RESULTS OF OPERATIONS

         Revenues

The Partnership's sole source of revenue for the three and nine months ended
September 30, 1996 and 1995 was the interest earned on the investments made with
the capital contributions received from the General Partner and the limited
partners of the Partnership (the "Limited Partners") prior to their disbursement
to Alkermes for research and development as well as other Partnership expenses.
Interest income for the three and nine months ended September 30, 1996 was $329
and $11,287 compared to $90,832 and $236,564 for the corresponding periods of
the prior year. Interest income for the three and nine months ended September
30, 1996 as compared to 1995 decreased as a result of the decrease in cash and
cash equivalents and short-term investments. The decrease in the cash and cash
equivalents and short-term investments of the Partnership are a result of the
substantial completion of the annual capital contributions by the Limited
Partners and the General Partner in 1995 and the completion of the development
funding to Alkermes during the quarter ended June 30, 1996.

         Expenses

Research and development expenses for the three and nine months ended September
30, 1996 were zero and $4,850,000 as compared to $2,698,000 and $8,284,000 for
the three and nine months ended September 30, 1995. The decrease in research and
development expenses was a result 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 and nine months ended
September 30, 1996 were $8,136 and $49,815 as compared to $41,369 and $102,153
for the three and nine months ended September 30, 1995. The decrease was mainly
a result of a decrease in amortization of organization costs and legal fees.

There was no interest expense for the three and nine months ended September 30,
1996 as compared to zero and $98,666 for the three and nine months ended
September 30, 1995. The decrease was a result of the repayment in April 1995 of
the $4,735,000 note payable to Alkermes.


                                      (7)
<PAGE>   8

LIQUIDITY AND CAPITAL RESOURCES

At September 30, 1996, the Partnership had current assets totaling $40,518,
consisting solely of cash; and current liabilities of $14,998.

The Partnership's primary source of funding and capital resources has been the
annual capital contributions by the Limited Partners and the General Partner.
The Limited Partners' capital contributions have been remitted to the
Partnership in four annual installment payments, the fourth and final payment of
which was due on April 15, 1995. During the six months ended June 30, 1996, the
Partnership received approximately $2,058,000 in cash as a result of the
purchase by Alkermes of previously defaulted Class A limited partnership units.
There will be no additional capital contributions received by the Partnership
after the quarter ended June 30, 1996.

The Partnership has used its capital resources primarily to fund the further
development and clinical testing of RMPs. Such development is being conducted
for the Partnership by Alkermes pursuant to the Product Development Agreement.
During the six months ended June 30, 1996, the Partnership completed its
development funding to Alkermes and incurred expenses totaling $4,850,000 for
reimbursable costs incurred by Alkermes. Alkermes anticipates that its clinical
testing of RMPs will continue beyond such date. Since none of the Partners of
the Partnership are obligated to make any further capital contributions to the
Partnership, Alkermes intends to fund the further development of RMPs.

The Partnership's remaining cash and equivalents will be used 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 after the Partnership's current assets are depleted,
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 September 30, 1996, the Partnership is expected to have no material
assets, liabilities or partners' capital and will have no future liquidity or
capital resources requirements other than those funded by Alkermes.

                                     (8)
<PAGE>   9

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.*

                       10.1      Product Development Agreement, dated as of
                                 March 6, 1992, between the Partnership and
                                 Alkermes.*

                       10.2      Purchase Agreement, dated as of March 6, 1992,
                                 by and among Alkermes and each of the Limited
                                 Partners, from time to time, of the
                                 Partnership.*

                       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, 1996.

                                      (9)
<PAGE>   10

                                   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 6, 1996             By: /s/ Richard F. Pops
                                      ------------------------------------------
                                       Richard F. Pops
                                       Director, President and Chief Executive
                                       Officer (Principal Executive Officer)



Date: November 6, 1996             By: /s/ Michael J. Landine
                                      ------------------------------------------
                                       Michael J. Landine
                                       Director, Vice President, Chief
                                       Financial Officer, Treasurer and
                                       Assistant Secretary (Principal
                                       Financial and Accounting Officer)



                                      (10)
<PAGE>   11
                                 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.*
        
                  10.1          Product Development Agreement, dated as of
                                March 6, 1992, between the Partnership and
                                Alkermes.*
        
                  10.2          Purchase Agreement, dated as of March 6, 1992,
                                by and among Alkermes and each of the Limited
                                Partners, from time to time, of the
                                Partnership.*
        
                  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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