<PAGE>   1

                                                          Registration No. 333-

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    FORM S-8
                             REGISTRATION STATEMENT
                        UNDER THE SECURITIES ACT OF 1933

                                 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, Massachusetts                       02139-4234 
------------------------------------------                   -------------------
(ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)                         (ZIP CODE)


                                 Alkermes, Inc.
                            Amended and Restated 1990
                      Omnibus Stock Option Plan, as Amended
                      -------------------------------------
                            (FULL TITLE OF THE PLAN)

                                 Richard F. Pops
                             Chief Executive Officer
                                 Alkermes, Inc.
                                64 Sidney Street
                       Cambridge, Massachusetts 02139-4234
                     ---------------------------------------
                     (NAME AND ADDRESS OF AGENT FOR SERVICE)

                                 (617) 494-0171
                      ---------------------------------------
                      (TELEPHONE NUMBER, INCLUDING AREA CODE,
                              OF AGENT FOR SERVICE)

                                with a copy to:

                          Morris Cheston, Jr., Esquire
                             Martha J. Hays, Esquire
                     Ballard Spahr Andrews & Ingersoll, LLP
                               1735 Market Street
                      Philadelphia, Pennsylvania 19103-7599
                                 (215) 665-8500


                         CALCULATION OF REGISTRATION FEE

<TABLE>
<CAPTION>
--------------------------------------------------------------------------------
                                       Proposed     Proposed
Title of                               Maximum      Maximum
Securities           Amount            Offering     Aggregate      Amount of
to be                to be             Price Per    Offering       Registration
Registered           Registered(1)     Share(2)     Price(2)       Fee
--------------------------------------------------------------------------------
<S>                  <C>               <C>          <C>            <C>   
Common Stock,
par value $.01
per share            750,000           $26.00       $19,500,000    $5,421
--------------------------------------------------------------------------------
</TABLE>



(1)  In addition, pursuant to Rule 416(a) under the Securities Act of 1933, this
     registration statement shall be deemed to cover an indeterminate number of
     additional shares of Common Stock issuable in the event the number of
     outstanding shares of the Company is increased by split-up,
     reclassification, stock dividend and the like.
(2)  Estimated solely for the purpose of calculating the registration fee. In
     accordance with Rule 457(h), the price shown is based upon the average of
     the high and low price of the Company's Common Stock on January 19, 1999,
     $26.00, as reported on the Nasdaq National Market for securities of the
     same class as those to be offered.


<PAGE>   2


     Part I and Items 4-7 and 9 of Part II of Alkermes, Inc.'s Registration
Statement on Form S-8 (File No. 33-44752) are incorporated by reference herein
pursuant to Instruction E of Form S-8.

          PART II - INFORMATION REQUIRED IN THE REGISTRATION STATEMENT


ITEM 3.   INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE.

          The following documents filed with the Securities and Exchange
Commission (the "Commission") pursuant to the Securities Exchange Act of 1934
(the "Exchange Act") by Alkermes, Inc. (the "Company") (File No. 0-19267) or
pursuant to the Securities Act of 1933, as amended (the "Securities Act") are
incorporated herein by reference:

          (a)  Annual Report on Form 10-K for the fiscal year ended March 31,
               1998;

          (b)  Quarterly Reports on Form 10-Q for the quarters ended June 30,
               1998, and September 30, 1998;

          (c)  Current Report on Form 8-K dated April 15, 1998; and

          (d)  Item 1 of Registration Statement of the Company on Form 8-A dated
               June 28, 1991, as amended by a Report on Form 8-A/A dated January
               17, 1997.

          All documents filed by the Company pursuant to Sections 13(a), 13(c),
14 or 15(d) of the Exchange Act, after the date of this Registration Statement
and prior to the termination of the offering, shall be deemed to be incorporated
by reference herein and to be part hereof from the date of filing such
documents. Any statement contained herein or in a document incorporated by
reference or deemed to be incorporated by reference herein shall be deemed to be
modified or superseded for purposes of this Registration Statement to the extent
that such statement is modified or superseded by any other subsequently filed
document which is incorporated or is deemed to be incorporated by reference
herein. Any such statement so modified or superseded shall not be deemed, except
as so modified or superseded, to constitute a part of this Registration
Statement.

ITEM 8.  EXHIBITS.

     4.1  Specimen of Stock Certificate of Alkermes, Inc. (Incorporated by
          reference to Exhibit 4 to the Registrant'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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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



                                      II-1


<PAGE>   3


     4.4  Amendment to 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 Registrant's
          Report on Form 10-Q for the quarter ended September 30, 1991).

     4.5  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 Registrant's Report on Form 10-Q for the quarter ended
          December 31, 1992).

     4.6  Amendment to 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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

     5    Opinion of Ballard Spahr Andrews & Ingersoll, LLP as to the legality
          of the securities to be offered.

     23.1 Consent of Ballard Spahr Andrews & Ingersoll, LLP (included as part of
          Exhibit 5).

     23.2 Consent of Deloitte & Touche LLP.

     24   Power of Attorney (included in signature page).



                                      II-2


<PAGE>   4


                                   SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Cambridge, Commonwealth of Massachusetts, on January
22, 1999


                                       ALKERMES, INC.


                                       By /s/ Richard F. Pops           
                                          ------------------------------
                                          Richard F. Pops
                                          Chief Executive Officer


     Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.

     Each person whose signature appears below in so signing also makes,
constitutes and appoints Richard F. Pops and James M. Frates, and each of them,
his true and lawful attorney-in-fact, with full power of substitution, for him
in any and all capacities, to execute and cause to be filed with the Securities
and Exchange Commission any and all amendments and post-effective amendments to
this Registration Statement, with exhibits thereto and other documents in
connection therewith, and hereby ratifies and confirms all that said
attorney-in-fact or his substitute or substitutes may do or cause to be done by
virtue hereof.


<TABLE>
<CAPTION>


     Signature                          Title                       Date
     ---------                          -----                       ----

<S>                                 <C>                       <C>
/s/ Michael A. Wall                 Director and              January 22, 1999
----------------------------        Chairman of the 
Michael A. Wall                     Board           



/s/ Richard F. Pops                 Director and Chief        January 22, 1999
----------------------------        Executive Officer 
Richard F. Pops                     (Principal        
                                    Executive Officer)


/s/ Robert A. Breyer                Director, President       January 22, 1999
----------------------------        and Chief Operating
Robert A. Breyer                    Officer            
</TABLE>



                                      II-3


<PAGE>   5



<TABLE>

<S>                                 <C>                        <C>

/s/ James M. Frates                 Vice President, Chief      January 22, 1999
---------------------------         Financial Officer and
James M. Frates                     Treasurer (Principal
                                    Financial Officer
                                    and Principal 
                                    Accounting Officer)


/s/ Floyd E. Bloom                  Director                   January 22, 1999
---------------------------
Floyd E. Bloom


/s/ John K. Clarke                  Director                   January 22, 1999
---------------------------
John K. Clarke


/s/ Alexander Rich                  Director                   January 22, 1999
---------------------------
Alexander Rich


/s/ Paul Schimmel                   Director                   January 22, 1999
---------------------------
Paul Schimmel
</TABLE>



                                      II-4

<PAGE>   6


                                  EXHIBIT INDEX



Number                     Exhibit
------                     -------

 4.1      Specimen of Stock Certificate of Alkermes, Inc. (Incorporated by
          reference to Exhibit 4 to the Registrant'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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

 4.4      Amendment to 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 Registrant's
          Report on Form 10-Q for the quarter ended September 30, 1991).

 4.5      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 Registrant's Report on Form 10-Q for the quarter ended
          December 31, 1992).

 4.6      Amendment to 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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

 5        Opinion of Ballard Spahr Andrews & Ingersoll, LLP as to the legality
          of the securities to be offered.

23.1      Consent of Ballard Spahr Andrews & Ingersoll, LLP (included as part of
          Exhibit 5).

23.2      Consent of Deloitte & Touche LLP.

24        Power of Attorney (included in signature page).
[{"type": "S-8", "sequence": "1", "description": "ALKERMES,INC.", "secsgml_size_bytes": 14180}]
{"company-data": {"conformed-name": "ALKERMES INC", "cik": "0000874663", "assigned-sic": "2834", "irs-number": "232472830", "state-of-incorporation": "PA", "fiscal-year-end": "0331"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-71011", "film-number": "99511435"}, "business-address": {"street1": "64 SIDNEY ST", "city": "CAMBRIDGE", "state": "MA", "zip": "02139-4136", "phone": "6174940171"}}
1

                                                          Registration No. 333-

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    FORM S-8
                             REGISTRATION STATEMENT
                        UNDER THE SECURITIES ACT OF 1933

                                 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, Massachusetts                       02139-4234 
------------------------------------------                   -------------------
(ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)                         (ZIP CODE)

                                 Alkermes, Inc.
                            Amended and Restated 1990
                      Omnibus Stock Option Plan, as Amended
                      -------------------------------------
                            (FULL TITLE OF THE PLAN)

                                 Richard F. Pops
                             Chief Executive Officer
                                 Alkermes, Inc.
                                64 Sidney Street
                       Cambridge, Massachusetts 02139-4234
                     ---------------------------------------
                     (NAME AND ADDRESS OF AGENT FOR SERVICE)

                                 (617) 494-0171
                      ---------------------------------------
                      (TELEPHONE NUMBER, INCLUDING AREA CODE,
                              OF AGENT FOR SERVICE)

                                with a copy to:

                          Morris Cheston, Jr., Esquire
                             Martha J. Hays, Esquire
                     Ballard Spahr Andrews & Ingersoll, LLP
                               1735 Market Street
                      Philadelphia, Pennsylvania 19103-7599
                                 (215) 665-8500

                         CALCULATION OF REGISTRATION FEE
--------------------------------------------------------------------------------
                                       Proposed     Proposed
Title of                               Maximum      Maximum
Securities           Amount            Offering     Aggregate      Amount of
to be                to be             Price Per    Offering       Registration
Registered           Registered(1)     Share(2)     Price(2)       Fee
--------------------------------------------------------------------------------
Common Stock,
par value $.01
per share            750,000           $26.00       $19,500,000    $5,421
--------------------------------------------------------------------------------
(1)  In addition, pursuant to Rule 416(a) under the Securities Act of 1933, this
     registration statement shall be deemed to cover an indeterminate number of
     additional shares of Common Stock issuable in the event the number of
     outstanding shares of the Company is increased by split-up,
     reclassification, stock dividend and the like.
(2)  Estimated solely for the purpose of calculating the registration fee. In
     accordance with Rule 457(h), the price shown is based upon the average of
     the high and low price of the Company's Common Stock on January 19, 1999,
     $26.00, as reported on the Nasdaq National Market for securities of the
     same class as those to be offered.
2

     Part I and Items 4-7 and 9 of Part II of Alkermes, Inc.'s Registration
Statement on Form S-8 (File No. 33-44752) are incorporated by reference herein
pursuant to Instruction E of Form S-8.

          PART II - INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.   INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE.

          The following documents filed with the Securities and Exchange
Commission (the "Commission") pursuant to the Securities Exchange Act of 1934
(the "Exchange Act") by Alkermes, Inc. (the "Company") (File No. 0-19267) or
pursuant to the Securities Act of 1933, as amended (the "Securities Act") are
incorporated herein by reference:

          (a)  Annual Report on Form 10-K for the fiscal year ended March 31,
               1998;

          (b)  Quarterly Reports on Form 10-Q for the quarters ended June 30,
               1998, and September 30, 1998;

          (c)  Current Report on Form 8-K dated April 15, 1998; and

          (d)  Item 1 of Registration Statement of the Company on Form 8-A dated
               June 28, 1991, as amended by a Report on Form 8-A/A dated January
               17, 1997.

          All documents filed by the Company pursuant to Sections 13(a), 13(c),
14 or 15(d) of the Exchange Act, after the date of this Registration Statement
and prior to the termination of the offering, shall be deemed to be incorporated
by reference herein and to be part hereof from the date of filing such
documents. Any statement contained herein or in a document incorporated by
reference or deemed to be incorporated by reference herein shall be deemed to be
modified or superseded for purposes of this Registration Statement to the extent
that such statement is modified or superseded by any other subsequently filed
document which is incorporated or is deemed to be incorporated by reference
herein. Any such statement so modified or superseded shall not be deemed, except
as so modified or superseded, to constitute a part of this Registration
Statement.

ITEM 8.  EXHIBITS.

     4.1  Specimen of Stock Certificate of Alkermes, Inc. (Incorporated by
          reference to Exhibit 4 to the Registrant'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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

                                      II-1
3

     4.4  Amendment to 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 Registrant's
          Report on Form 10-Q for the quarter ended September 30, 1991).

     4.5  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 Registrant's Report on Form 10-Q for the quarter ended
          December 31, 1992).

     4.6  Amendment to 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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

     5    Opinion of Ballard Spahr Andrews & Ingersoll, LLP as to the legality
          of the securities to be offered.

     23.1 Consent of Ballard Spahr Andrews & Ingersoll, LLP (included as part of
          Exhibit 5).

     23.2 Consent of Deloitte & Touche LLP.

     24   Power of Attorney (included in signature page).

                                      II-2
4

                                   SIGNATURES

     Pursuant to the requirements of the Securities Act of 1933, the registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Cambridge, Commonwealth of Massachusetts, on January
22, 1999

                                       ALKERMES, INC.

                                       By /s/ Richard F. Pops           
                                          ------------------------------
                                          Richard F. Pops
                                          Chief Executive Officer

     Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.

     Each person whose signature appears below in so signing also makes,
constitutes and appoints Richard F. Pops and James M. Frates, and each of them,
his true and lawful attorney-in-fact, with full power of substitution, for him
in any and all capacities, to execute and cause to be filed with the Securities
and Exchange Commission any and all amendments and post-effective amendments to
this Registration Statement, with exhibits thereto and other documents in
connection therewith, and hereby ratifies and confirms all that said
attorney-in-fact or his substitute or substitutes may do or cause to be done by
virtue hereof.
Signature                          Title                       Date
     ---------                          -----                       ----
/s/ Michael A. Wall                 Director and              January 22, 1999
----------------------------        Chairman of the 
Michael A. Wall                     Board           

/s/ Richard F. Pops                 Director and Chief        January 22, 1999
----------------------------        Executive Officer 
Richard F. Pops                     (Principal        
                                    Executive Officer)

/s/ Robert A. Breyer                Director, President       January 22, 1999
----------------------------        and Chief Operating
Robert A. Breyer                    Officer
II-3
5
/s/ James M. Frates                 Vice President, Chief      January 22, 1999
---------------------------         Financial Officer and
James M. Frates                     Treasurer (Principal
                                    Financial Officer
                                    and Principal 
                                    Accounting Officer)

/s/ Floyd E. Bloom                  Director                   January 22, 1999
---------------------------
Floyd E. Bloom

/s/ John K. Clarke                  Director                   January 22, 1999
---------------------------
John K. Clarke

/s/ Alexander Rich                  Director                   January 22, 1999
---------------------------
Alexander Rich

/s/ Paul Schimmel                   Director                   January 22, 1999
---------------------------
Paul Schimmel
II-4
6

                                  EXHIBIT INDEX

Number                     Exhibit
------                     -------

 4.1      Specimen of Stock Certificate of Alkermes, Inc. (Incorporated by
          reference to Exhibit 4 to the Registrant'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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

 4.4      Amendment to 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 Registrant's
          Report on Form 10-Q for the quarter ended September 30, 1991).

 4.5      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 Registrant's Report on Form 10-Q for the quarter ended
          December 31, 1992).

 4.6      Amendment to 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 Registrant's
          Registration Statement on Form S-3 (File No. 333-50157)).

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

 5        Opinion of Ballard Spahr Andrews & Ingersoll, LLP as to the legality
          of the securities to be offered.

23.1      Consent of Ballard Spahr Andrews & Ingersoll, LLP (included as part of
          Exhibit 5).

23.2      Consent of Deloitte & Touche LLP.

24        Power of Attorney (included in signature page).