content: <PAGE>   1
   As filed with the Securities and Exchange Commission on September 19, 1996
  
                                                    Registration No. 333-_________
  
  - --------------------------------------------------------------------------------
  
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
  
                                    FORM S-8
  
                             REGISTRATION STATEMENT
                                    under the
                             SECURITIES ACT OF 1933
  
                       VERTEX PHARMACEUTICALS INCORPORATED
             ------------------------------------------------------
             (Exact name of registrant as specified in its charter)
  
            Massachusetts                                 04-3039129
  - ----------------------------------------    ------------------------------------
  (State of incorporation or organization)    (I.R.S. Employer Identification No.)
  
                 130 Waverly Street, Cambridge, Massachusetts 02139
                 --------------------------------------------------
                      (Address of Principal Executive Offices)
  
                         Vertex Pharmaceuticals Incorporated
                            EMPLOYEE STOCK PURCHASE PLAN
                            ----------------------------
                              (Full title of the plan)
  
                  Joshua Boger, President & Chief Executive Officer
                         Vertex Pharmaceuticals Incorporated
                                 130 Waverly Street
                              Cambridge, MA 02139-4242
                              ------------------------
                       (Name and address of agent for service)
  
                                   (617) 577-6000
            -------------------------------------------------------------
            (Telephone number, including area code, of agent for service)
  <TABLE>
                                           CALCULATION OF REGISTRATION FEE
  ==================================================================================================================
  <CAPTION>
                                                   Proposed Maximum        Proposed Maximum
  Title of Securities          Amount to be        Offering Price          Aggregate                Amount of
  to be Registered             Registered (1)      Per Share (2)           Offering Price (2)       Registration Fee
  - -----------------            --------------      -------------           ------------------       ----------------
  <S>                             <C>                  <C>                     <C>                      <C>
  Common Stock, par
  value, $.01 per share           150,000              $33.31                   $4,996,500               $1,723
  
  Rights to purchase
  Series A Junior Participating
  Preferred Stock                      (3)                 (3)                          (3)                None
  - ------------------------------------------------------------------------------------------------------------------
  <FN>
  
  (1)  Together with an indeterminate number of additional shares which may result from a stock split, stock dividend, 
       or other similar adjustment of the outstanding shares of Common Stock.
  
  (2)  Computed solely for the purpose of calculating the registration fee on the basis of the average of the high and 
       low prices per share of the Registrant's Common Stock on the Nasdaq National Market System as of a date 
       (September 17, 1996) within five (5) business days prior to filing this Registration Statement.
  
  (3)  No separate consideration will be received for the Rights.
  </TABLE>
  
  <PAGE>   2
  
  
    Statement Regarding Incorporation By Reference From Effective Registration
    --------------------------------------------------------------------------
                                  Statement
                                  ---------
  
       Pursuant to Instruction E to Form S-8, the contents of Items 3 through 7
  and 9 of the Registrant's Registration Statement on Form S-8 filed with the
  S.E.C. on June 4, 1992 (Registration No. 33-48348) are incorporated by reference
  in this Registration Statement. For Item 8, see the Exhibit Index immediately
  following the signature page of this Registration Statement.
  
                                      -Page 2-
  <PAGE>   3
  
  
                                     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 Cambridge, Massachusetts, on September 19, 1996.
  
                                         VERTEX PHARMACEUTICALS INCORPORATED
  
  
                                         By: /s/ Joshua S. Boger
                                             -------------------------------------
                                             Joshua S. Boger
                                             President and Chief Executive Officer
  
  
       KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
  below constitutes and appoints Joshua S. Boger, Richard H. Aldrich, and Thomas
  G. Auchincloss, Jr., and each of them, his true and lawful attorneys-in-fact and
  agents, with full power of substitution and resubstitution in each of them, for
  him and in his name, place and stead, and in any and all capacities, to sign any
  and all amendments (including post-effective amendments) to this Registration
  Statement, and to file the same, with all exhibits thereto and other documents
  in connection therewith, with the Securities and Exchange Commission, granting
  unto said attorneys-in-fact and agents, and each of them, full power and
  authority to do and perform each and every act and thing requisite or necessary
  to be done in and about the premises, as fully to all intents and purposes as he
  might or could do in person, hereby ratifying and confirming all that said
  attorneys-in-fact and agents or any of them or their or his substitute or
  substitutes may lawfully do or cause to be done by virtue hereof.
  <TABLE>
       Pursuant to the requirements of the Securities Act of 1933, this
  Registration Statement has been signed by the following persons in the
  capacities and on the dates indicated.
  <S>                                 <C>                                         <C>
  /s/ Joshua S. Boger                 Director, President and                     September 19, 1996
  - ---------------------------------   Chief Executive Officer                     ------------
  Joshua S. Boger                     (Principal Executive Officer) 
  
  /s/ Thomas G. Auchincloss, Jr.      Senior Director of Finance and              September 19, 1996
  - ---------------------------------   Treasurer (Principal Financial Officer)     ------------
  Thomas G. Auchincloss, Jr.         
  
  /s/ Hans D. Van Houte               Controller                                  September 19, 1996
  - ---------------------------------                                               ------------
  Hans D. Van Houte
  
  /s/ Barry M. Bloom                  Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Barry M. Bloom
  
  /s/ Roger W. Brimblecombe           Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Roger W. Brimblecombe
  
  /s/ Donald R. Conklin               Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Donald R. Conklin
  
  /s/ William W. Helman IV            Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  William W. Helman IV
  
  /s/ Benno C. Schmidt                Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Benno C. Schmidt
  
  </TABLE>
                                      -Page 3-
  
  <PAGE>   4
  
  
                                     EXHIBITS
  
  
  Exhibit No.                      Description
  - -----------                      -----------
  
  (4.1)   Specimen Common Stock Certificate (filed as Exhibit 4.1 to the
          Registration Statement on Form S-1, Registration No. 33-40966, as
          amended, and incorporated herein by reference)
  
  (4.2)   Stockholder Rights Plan (filed as Exhibit 4.2 to the Registration
          Statement on Form S-1, Registration No. 33-40966, as amended, and
          incorporated herein by reference)
  
  (5)     Opinion of Warner & Stackpole LLP (filed herewith at page 5)
  
  (23.1)  Consent of Coopers & Lybrand LLP (filed herewith at page 7)
  
  (23.2)  Consent of Warner & Stackpole LLP (included in Exhibit 5)
  
  (24)    Power of Attorney to file future amendments (included on the signature
          page of this Registration Statement)
  
  (99.1)  Amendment to the Company's Employee Stock Purchase Plan approved by the
          Stockholders on May 9, 1996 (filed herewith at page 8).
  
  
                                      -Page 4-
metadata_documents: [{"type": "S-8", "sequence": "1", "description": "VERTEX PHARMACEUTICALS INCORPORATED", "secsgml_size_bytes": 9389}]
metadata_filer: {"company-data": {"conformed-name": "VERTEX PHARMACEUTICALS INC / MA", "cik": "0000875320", "assigned-sic": "2834", "irs-number": "043039129", "state-of-incorporation": "MA", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-12325", "film-number": "96632278"}, "business-address": {"street1": "40 ALLSTON ST", "city": "CAMBRIDGE", "state": "MA", "zip": "02139", "phone": "6175763111"}}
text: 1
   As filed with the Securities and Exchange Commission on September 19, 1996
  
                                                    Registration No. 333-_________
  
  - --------------------------------------------------------------------------------
  
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
  
                                    FORM S-8
  
                             REGISTRATION STATEMENT
                                    under the
                             SECURITIES ACT OF 1933
  
                       VERTEX PHARMACEUTICALS INCORPORATED
             ------------------------------------------------------
             (Exact name of registrant as specified in its charter)
  
            Massachusetts                                 04-3039129
  - ----------------------------------------    ------------------------------------
  (State of incorporation or organization)    (I.R.S. Employer Identification No.)
  
                 130 Waverly Street, Cambridge, Massachusetts 02139
                 --------------------------------------------------
                      (Address of Principal Executive Offices)
  
                         Vertex Pharmaceuticals Incorporated
                            EMPLOYEE STOCK PURCHASE PLAN
                            ----------------------------
                              (Full title of the plan)
  
                  Joshua Boger, President & Chief Executive Officer
                         Vertex Pharmaceuticals Incorporated
                                 130 Waverly Street
                              Cambridge, MA 02139-4242
                              ------------------------
                       (Name and address of agent for service)
  
                                   (617) 577-6000
            -------------------------------------------------------------
            (Telephone number, including area code, of agent for service)
  
                                           CALCULATION OF REGISTRATION FEE
  ==================================================================================================================
  Proposed Maximum        Proposed Maximum
  Title of Securities          Amount to be        Offering Price          Aggregate                Amount of
  to be Registered             Registered (1)      Per Share (2)           Offering Price (2)       Registration Fee
  - -----------------            --------------      -------------           ------------------       ----------------
  Common Stock, par
  value, $.01 per share           150,000              $33.31                   $4,996,500               $1,723
  
  Rights to purchase
  Series A Junior Participating
  Preferred Stock                      (3)                 (3)                          (3)                None
  - ------------------------------------------------------------------------------------------------------------------
  (1)  Together with an indeterminate number of additional shares which may result from a stock split, stock dividend, 
       or other similar adjustment of the outstanding shares of Common Stock.
  
  (2)  Computed solely for the purpose of calculating the registration fee on the basis of the average of the high and 
       low prices per share of the Registrant's Common Stock on the Nasdaq National Market System as of a date 
       (September 17, 1996) within five (5) business days prior to filing this Registration Statement.
  
  (3)  No separate consideration will be received for the Rights.
  2
  
    Statement Regarding Incorporation By Reference From Effective Registration
    --------------------------------------------------------------------------
                                  Statement
                                  ---------
  
       Pursuant to Instruction E to Form S-8, the contents of Items 3 through 7
  and 9 of the Registrant's Registration Statement on Form S-8 filed with the
  S.E.C. on June 4, 1992 (Registration No. 33-48348) are incorporated by reference
  in this Registration Statement. For Item 8, see the Exhibit Index immediately
  following the signature page of this Registration Statement.
  
                                      -Page 2-
  3
  
                                     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 Cambridge, Massachusetts, on September 19, 1996.
  
                                         VERTEX PHARMACEUTICALS INCORPORATED
  
                                         By: /s/ Joshua S. Boger
                                             -------------------------------------
                                             Joshua S. Boger
                                             President and Chief Executive Officer
  
       KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
  below constitutes and appoints Joshua S. Boger, Richard H. Aldrich, and Thomas
  G. Auchincloss, Jr., and each of them, his true and lawful attorneys-in-fact and
  agents, with full power of substitution and resubstitution in each of them, for
  him and in his name, place and stead, and in any and all capacities, to sign any
  and all amendments (including post-effective amendments) to this Registration
  Statement, and to file the same, with all exhibits thereto and other documents
  in connection therewith, with the Securities and Exchange Commission, granting
  unto said attorneys-in-fact and agents, and each of them, full power and
  authority to do and perform each and every act and thing requisite or necessary
  to be done in and about the premises, as fully to all intents and purposes as he
  might or could do in person, hereby ratifying and confirming all that said
  attorneys-in-fact and agents or any of them or their or his substitute or
  substitutes may lawfully do or cause to be done by virtue hereof.
  
       Pursuant to the requirements of the Securities Act of 1933, this
  Registration Statement has been signed by the following persons in the
  capacities and on the dates indicated.
  /s/ Joshua S. Boger                 Director, President and                     September 19, 1996
  - ---------------------------------   Chief Executive Officer                     ------------
  Joshua S. Boger                     (Principal Executive Officer) 
  
  /s/ Thomas G. Auchincloss, Jr.      Senior Director of Finance and              September 19, 1996
  - ---------------------------------   Treasurer (Principal Financial Officer)     ------------
  Thomas G. Auchincloss, Jr.         
  
  /s/ Hans D. Van Houte               Controller                                  September 19, 1996
  - ---------------------------------                                               ------------
  Hans D. Van Houte
  
  /s/ Barry M. Bloom                  Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Barry M. Bloom
  
  /s/ Roger W. Brimblecombe           Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Roger W. Brimblecombe
  
  /s/ Donald R. Conklin               Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Donald R. Conklin
  
  /s/ William W. Helman IV            Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  William W. Helman IV
  
  /s/ Benno C. Schmidt                Director                                    September 19, 1996
  - ---------------------------------                                               ------------
  Benno C. Schmidt
  -Page 3-
  4
  
                                     EXHIBITS
  
  Exhibit No.                      Description
  - -----------                      -----------
  
  (4.1)   Specimen Common Stock Certificate (filed as Exhibit 4.1 to the
          Registration Statement on Form S-1, Registration No. 33-40966, as
          amended, and incorporated herein by reference)
  
  (4.2)   Stockholder Rights Plan (filed as Exhibit 4.2 to the Registration
          Statement on Form S-1, Registration No. 33-40966, as amended, and
          incorporated herein by reference)
  
  (5)     Opinion of Warner & Stackpole LLP (filed herewith at page 5)
  
  (23.1)  Consent of Coopers & Lybrand LLP (filed herewith at page 7)
  
  (23.2)  Consent of Warner & Stackpole LLP (included in Exhibit 5)
  
  (24)    Power of Attorney to file future amendments (included on the signature
          page of this Registration Statement)
  
  (99.1)  Amendment to the Company's Employee Stock Purchase Plan approved by the
          Stockholders on May 9, 1996 (filed herewith at page 8).
  
                                      -Page 4-