<PAGE>


    As filed with the Securities and Exchange Commission on September 10, 1997
                                                Registration No. 333-


                          SECURITIES AND EXCHANGE COMMISSION
                                WASHINGTON, D.C. 20549

                                ----------------------
                                           
                                       FORM S-8
                             REGISTRATION STATEMENT UNDER
                              THE SECURITIES ACT OF 1933
                                           
                                   AFFYMETRIX, INC.      
                -----------------------------------------------------
                (Exact Name of Registrant as Specified in Its Charter)
                                           
           California                                    77-0319159  
 -------------------------------                     ------------------
 (State or Other Jurisdiction of                      (I.R.S. Employer
  Incorporation or Organization)                     Identification No.) 
                                           
               3380 Central Expressway, Santa Clara, California 95051 
               ------------------------------------------------------
                       (Address of Principal Executive Offices)
                                           
                                  1993 Stock Plan      
                               ------------------------
                               (Full Title of the Plan)

                                  Vernon A. Norviel
                          Vice President and General Counsel
                                   Affymetrix, Inc.
                3380 Central Expressway, Santa Clara, California 95051
                ------------------------------------------------------
                       (Name and Address of Agent For Service)
                                           
                                   (408) 731-5000                        
            ------------------------------------------------------------
            (Telephone Number, Including Area Code, of Agent For Service)
                                           
                         Copy to:  Stephen C. Ferruolo, Esq.
                           Heller Ehrman White & McAuliffe
                                525 University Avenue
                          Palo Alto, California  94301-1908
                                    (415) 324-7000
                                           
<TABLE>
<CAPTION>

                                      CALCULATION OF REGISTRATION FEE
- --------------------------------------------------------------------------------------------------
- --------------------------------------------------------------------------------------------------
                                           Proposed             Proposed              
      Title of            Amount            Maximum              Maximum              Amount of
     Securities            to be         Offering Price     Aggregate Offering       Registration
  to be Registered       Registered       per Share (1)            Price                 Fee     
- --------------------------------------------------------------------------------------------------
<S>                      <C>             <C>                <C>                      <C>       
Common Stock, no          1,500,000        $  34.07             $51,093,750            $15,482    
     par value                             
- --------------------------------------------------------------------------------------------------
- --------------------------------------------------------------------------------------------------
</TABLE>

(1) Estimated solely for the purpose of computing the amount of registration
    fee pursuant to Rule 457(c) under the Securities Act of 1933, as amended,
    based on the average of the high and low prices of the Registrant's Common
    Stock reported on the Nasdaq National Market on September 4, 1997.



<PAGE>


                                       PART II

                  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT


ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE

         The following documents filed or to be filed with the Securities and
Exchange Commission (the "Commission") by the registrant are incorporated by
reference in this registration statement:

         (a)  The registrant's Annual Report on Form 10-K for the fiscal year
ended December 31, 1996, and the registrant's Quarterly Reports on Form 10-Q for
the fiscal quarters ended March 31, 1997 and June 30, 1997;

         (b)  The registrant's Registration Statement on Form S-1 (No. 
333-3648) filed with the Commission on April 15, 1996, as amended;

         (c)  The description of the Common Stock of the registrant contained
in the registrant's Registration Statement on Form 8-A (No. 0-28218) filed with
the Commission on April 16, 1996 pursuant to Section 12 of the Exchange Act of
1934, as amended (the "Exchange Act"); and

         (d)  All documents subsequently filed by the registrant pursuant to
Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to the filing of
a post-effective amendment which indicates that all securities offered hereby
have been sold or which deregisters all securities then remaining unsold.

ITEM 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL.

    The validity of the Common Stock offered hereby will be passed upon for the
registrant by Heller Ehrman White & McAuliffe, Palo Alto, California.  As of the
date of this Registration Statement, members of Heller Ehrman White & McAuliffe
who are directly involved in the representation of the registrant beneficially
own approximately 13,300 shares of the registrant's Common Stock.

ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

    Pursuant to Section 204(a) and 317 of the California Corporations Code, as
amended, the registrant has included in its articles of incorporation and
by-laws provisions regarding the indemnification of officers and directors of
the registrant.  Article Four of registrant's Amended and Restated Articles of
Incorporation provides as follows:

    "The liability of the directors of this corporation for monetary damages
shall be eliminated to the fullest extent permissible under California law. 
This corporation is also authorized, to the fullest extent permissible under
California 


                                  II-2
<PAGE>

law, to indemnify its agents (as defined in Section 317 of the California 
Corporations Code), whether by by-law, agreement or otherwise, in excess of 
the indemnification expressly permitted by Section 317 and to advance defense 
expenses to its agents in connection with such matters as they are incurred, 
subject to the limits on such excess indemnification set forth in Section 204 
of the California Corporations Code.  If, after the effective date of this 
Article, California law is amended in a manner which permits a corporation to 
limit the monetary or other liability of its directors or to authorize 
indemnification of, or advancement of such defense expense to, its directors 
or other persons, in any such case to a greater extent than is permitted on 
such effective date, the references in this Article to "California law" shall 
to that extent be deemed to refer to California law as so amended."

    Section 29 of the registrant's By-Laws, as amended, provides as follows:

    "29.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

    (a)  INDEMNIFICATION.  To the fullest extent permissible under California 
law, the corporation shall indemnify its directors and officers against all 
expenses, judgment, fines settlement and other amounts actually and 
reasonably incurred by them in connection with any proceeding, including an 
action by or in the right of the corporation, by reason of the fact that such 
person is or was a director or officer of the corporation, or is or was 
serving at the request of the corporation as a director, officer, trustee, 
employee or agent of another corporation, or of a partnership, joint venture, 
trust or other enterprise (including service with respect to employee benefit 
plans).  To the fullest extent permissible under California law, expenses 
incurred by a director or officer seeking indemnification under this By-law 
in defending any proceeding shall be advanced by the corporation as they are 
incurred upon receipt by the corporation of an undertaking by or on behalf of 
the director or officer to repay such amount if it shall ultimately be 
determined that the director or officer is not entitled to be indemnified by 
the corporation for those expenses. If, after the effective date of this 
By-law, California law is amended in a manner which permits the corporation 
to authorize indemnification of or advancement of expenses to its directors 
or officers, in any such case to a greater extent than is permitted on such 
effective date, the references in this By-law to "California law" shall to 
that extent be deemed to refer to California law as so amended.  The rights 
granted by this By-law are contractual in nature and, as such, may not be 
altered with respect to any present or former director or officer without the 
written consent of that person.

    (b)  PROCEDURE.  Upon written request to the Board of Directors by a person
seeking indemnification under this By-law, the Board shall promptly determine in
accordance with Section 317(e) of the California Corporations Code whether the
applicable standard of conduct has been met and, if so, the Board shall
authorize indemnification.  If the Board cannot authorize 


                                  II-3
<PAGE>

indemnification because the number of directors who are parties to the 
proceeding with respect to which indemnification is sought prevents the 
formation of a quorum of directors who are not parties to the proceeding, 
then, upon written request by the person seeking indemnification, independent 
legal counsel (by means of a written opinion obtained at the corporation's 
expense) or the corporation's shareholders shall determine whether the 
applicable standard of conduct has been met and, if so, shall authorize 
indemnification.

    (c)  DEFINITIONS.  The term "proceeding" means any threatened, pending or 
completed action or proceeding, whether civil, criminal, administrative or 
investigative.  The term "expenses" includes, without limitation, attorney's 
fees and any expenses of establishing a right to indemnification."

    The registrant has entered into indemnification agreements with each of 
its current directors and officers or persons controlling the Registrant 
pursuant to the foregoing provisions.

ITEM 8.  EXHIBITS

  5.1    Opinion of Heller Ehrman White & McAuliffe

 23.1    Consent of Ernst & Young LLP, Independent Auditors

 23.3    Consent of Heller Ehrman White & McAuliffe
         (filed as part of Exhibit 5.1)

 24.1    Power of Attorney (See page II-6)

 99.1    1993 Stock Plan, as amended

ITEM 9.  UNDERTAKINGS

    A.   The undersigned registrant hereby undertakes:

         (1)  To file, during any period in which offers or sales are being
made, a post-effective amendment to this registration statement;

              (i)  To include any prospectus required by Section 10(a)(3) of
    the Securities Act of 1933, as amended (the "Securities Act");

              (ii) To reflect in the prospectus any facts or events arising
    after the effective date of the registration statement (or the most recent
    post-effective amendment thereof) which, individually or in the aggregate,
    represent a fundamental change in the information set forth in the
    registration statement;

              (iii)    To include any material information with respect to the
    plan of distribution not previously disclosed in the registration statement
    or any material change to such information in the registration statement;


                                  II-4
<PAGE>

PROVIDED, HOWEVER, that paragraphs A(1)(i) and A(1)(ii) do not apply if the
information required to be included in a post-effective amendment by those
paragraphs is contained in periodic reports filed by the registrant pursuant to
Section 13 or 15(d) of the Exchange Act that are incorporated by reference in
the registration statement.

         (2)  That, for the purpose of determining any liability under the
Securities Act, each such post-effective amendment shall be deemed to be a new
registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial BONA
FIDE offering thereof.

         (3)  To remove from registration by means of a post-effective
amendment any of the securities being registered which remain unsold at the
termination of the offering.

    B.   The undersigned registrant hereby undertakes that, for purposes of
determining liability under the Securities Act, each filing of the registrant's
annual report pursuant to Section 13(a) or 15(d) of the Exchange Act that is
incorporated by reference in the registration statement shall be deemed a new
registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial BONA
FIDE offering thereof.

    C.   Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the registrant pursuant to the foregoing provisions, or otherwise, the
registrant has been advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as expressed in the
Securities Act and is, therefore, unenforceable.  In the event that a claim for
indemnification against such liabilities (other than the payment by the
registrant of expenses incurred or paid by a director, officer or controlling
person of the registrant in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the registrant will, unless in
the opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Securities
Act and will be governed by the final adjudication of such issue.


                                  II-5
<PAGE>

                                SIGNATURES

         Pursuant to the requirements of the Securities Act, 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 Santa Clara, State of California, on this 28th day of
August, 1997.

                                  AFFYMETRIX, INC.



                                  By: /s/ Stephen P.A. Fodor
                                     --------------------------------------
                                     Stephen P.A. Fodor, Ph.D.
                                     President & Chief Executive Officer
                                     (Principal Executive Officer)



                         POWER OF ATTORNEY TO SIGN AMENDMENTS

         KNOW ALL MEN BY THESE PRESENTS, that each person whose signature
appears below does hereby constitute and appoint Stephen P.A. Fodor, Ph.D. and
Edward M. Hurwitz, or either or them, each with full power of substitution, such
person's true and lawful attorneys-in-fact and agents for such person in such
person's name, place and stead, in any and all capacities, to sign any or all
amendments (including post-effective amendments) to this Registration Statement
on Form S-8 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 full power and authority to do and
perform each and every act and thing requisite and necessary to be done in and
about the premises in order to effectuate the same as fully, to all intents and
purposes, as he or such person might or could do in person, hereby ratifying and
confirming all that said attorneys-in-fact and agents may lawfully do or cause
to be done by virtue hereof.

         Pursuant to the requirements of the Securities Act, this Registration
Statement on Form S-8 has been signed by the following persons in the capacities
and on the dates indicated.



                                  II-6
<PAGE>


       SIGNATURE                       CAPACITY                    DATE     
       ---------                       --------                    ----


/s/ Stephen P.A. Fodor
_____________________________     DIRECTOR, PRESIDENT AND     AUGUST 28, 1997
 STEPHEN P.A. FODOR, PH.D.        CHIEF EXECUTIVE OFFICER
                                  (PRINCIPAL EXECUTIVE 
                                  OFFICER)


_____________________________     DIRECTOR AND CHAIRMAN
    JOHN D. DIEKMAN PH.D.


/s/ Paul Berg
_____________________________     DIRECTOR                    AUGUST 25, 1997
     PAUL BERG, PH.D.


/s/ Douglas M. Hurt
_____________________________     DIRECTOR                    AUGUST 25, 1997
      DOUGLAS M. HURT


/s/ Vernon R. Louks, Jr.
_____________________________     DIRECTOR                    AUGUST 27, 1997
   VERNON R. LOUCKS, JR.


/s/ Barry C. Ross
_____________________________     DIRECTOR                    AUGUST 28, 1997
   BARRY C. ROSS, PH.D.


/s/ David B. Singer
_____________________________     DIRECTOR                    AUGUST 25, 1997
      DAVID B. SINGER


/s/ Lubert Stryer
_____________________________     DIRECTOR                    AUGUST 25, 1997
    LUBERT STRYER, M.D.


/s/ John A. Young
_____________________________     DIRECTOR                    AUGUST 28, 1997
       JOHN A. YOUNG



_____________________________     DIRECTOR
ALEJANDRO C. ZAFFARONI, PH.D.



                                    II-7

<PAGE>

/s/ Edward M. Hurwitz
______________________________    VICE PRESIDENT AND          AUGUST 29, 1997
        EDWARD M. HURWITZ         CHIEF FINANCIAL OFFICER
                                  (PRINCIPAL FINANCIAL
                                  OFFICER)



                                    II-8

<PAGE>

                                  INDEX TO EXHIBITS

                                                                 Sequentially
 Item                                                              Numbered
  No.                  Description of Item                            Page 
- ------   ------------------------------------------------------  ------------

  5.1    Opinion of Heller Ehrman White & McAuliffe

 23.1    Consent of Ernst & Young LLP, Independent Auditors

 23.3    Consent of Heller Ehrman White & McAuliffe
         (filed as part of Exhibit 5.1)

 24.1    Power of Attorney (see page II-6) 

 99.1    1993 Stock Plan, as amended
[{"type": "S-8", "sequence": "1", "description": "S-8", "secsgml_size_bytes": 19301}]
{"company-data": {"conformed-name": "AFFYMETRIX INC", "cik": "0000913077", "assigned-sic": "8731", "irs-number": "770319159", "state-of-incorporation": "CA", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "file-number": "333-35287", "film-number": "97678143"}, "business-address": {"street1": "3380 CENTRAL EXPRESSWAY", "city": "SANTA CLARA", "state": "CA", "zip": "95051", "phone": "4085226000"}, "mail-address": {"street1": "3380 CENTRAL EXPRESSWAY", "city": "SANTA CLARA", "state": "CA", "zip": "95051"}}
As filed with the Securities and Exchange Commission on September 10, 1997
                                                Registration No. 333-

                          SECURITIES AND EXCHANGE COMMISSION
                                WASHINGTON, D.C. 20549

                                ----------------------
                                           
                                       FORM S-8
                             REGISTRATION STATEMENT UNDER
                              THE SECURITIES ACT OF 1933
                                           
                                   AFFYMETRIX, INC.      
                -----------------------------------------------------
                (Exact Name of Registrant as Specified in Its Charter)
                                           
           California                                    77-0319159  
 -------------------------------                     ------------------
 (State or Other Jurisdiction of                      (I.R.S. Employer
  Incorporation or Organization)                     Identification No.) 
                                           
               3380 Central Expressway, Santa Clara, California 95051 
               ------------------------------------------------------
                       (Address of Principal Executive Offices)
                                           
                                  1993 Stock Plan      
                               ------------------------
                               (Full Title of the Plan)

                                  Vernon A. Norviel
                          Vice President and General Counsel
                                   Affymetrix, Inc.
                3380 Central Expressway, Santa Clara, California 95051
                ------------------------------------------------------
                       (Name and Address of Agent For Service)
                                           
                                   (408) 731-5000                        
            ------------------------------------------------------------
            (Telephone Number, Including Area Code, of Agent For Service)
                                           
                         Copy to:  Stephen C. Ferruolo, Esq.
                           Heller Ehrman White & McAuliffe
                                525 University Avenue
                          Palo Alto, California  94301-1908
                                    (415) 324-7000
CALCULATION OF REGISTRATION FEE
- --------------------------------------------------------------------------------------------------
- --------------------------------------------------------------------------------------------------
                                           Proposed             Proposed              
      Title of            Amount            Maximum              Maximum              Amount of
     Securities            to be         Offering Price     Aggregate Offering       Registration
  to be Registered       Registered       per Share (1)            Price                 Fee     
- --------------------------------------------------------------------------------------------------
Common Stock, no          1,500,000        $  34.07             $51,093,750            $15,482    
     par value                             
- --------------------------------------------------------------------------------------------------
- --------------------------------------------------------------------------------------------------
(1) Estimated solely for the purpose of computing the amount of registration
    fee pursuant to Rule 457(c) under the Securities Act of 1933, as amended,
    based on the average of the high and low prices of the Registrant's Common
    Stock reported on the Nasdaq National Market on September 4, 1997.
PART II

                  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE

         The following documents filed or to be filed with the Securities and
Exchange Commission (the "Commission") by the registrant are incorporated by
reference in this registration statement:

         (a)  The registrant's Annual Report on Form 10-K for the fiscal year
ended December 31, 1996, and the registrant's Quarterly Reports on Form 10-Q for
the fiscal quarters ended March 31, 1997 and June 30, 1997;

         (b)  The registrant's Registration Statement on Form S-1 (No. 
333-3648) filed with the Commission on April 15, 1996, as amended;

         (c)  The description of the Common Stock of the registrant contained
in the registrant's Registration Statement on Form 8-A (No. 0-28218) filed with
the Commission on April 16, 1996 pursuant to Section 12 of the Exchange Act of
1934, as amended (the "Exchange Act"); and

         (d)  All documents subsequently filed by the registrant pursuant to
Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to the filing of
a post-effective amendment which indicates that all securities offered hereby
have been sold or which deregisters all securities then remaining unsold.

ITEM 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL.

    The validity of the Common Stock offered hereby will be passed upon for the
registrant by Heller Ehrman White & McAuliffe, Palo Alto, California.  As of the
date of this Registration Statement, members of Heller Ehrman White & McAuliffe
who are directly involved in the representation of the registrant beneficially
own approximately 13,300 shares of the registrant's Common Stock.

ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

    Pursuant to Section 204(a) and 317 of the California Corporations Code, as
amended, the registrant has included in its articles of incorporation and
by-laws provisions regarding the indemnification of officers and directors of
the registrant.  Article Four of registrant's Amended and Restated Articles of
Incorporation provides as follows:

    "The liability of the directors of this corporation for monetary damages
shall be eliminated to the fullest extent permissible under California law. 
This corporation is also authorized, to the fullest extent permissible under
California 

                                  II-2
law, to indemnify its agents (as defined in Section 317 of the California 
Corporations Code), whether by by-law, agreement or otherwise, in excess of 
the indemnification expressly permitted by Section 317 and to advance defense 
expenses to its agents in connection with such matters as they are incurred, 
subject to the limits on such excess indemnification set forth in Section 204 
of the California Corporations Code.  If, after the effective date of this 
Article, California law is amended in a manner which permits a corporation to 
limit the monetary or other liability of its directors or to authorize 
indemnification of, or advancement of such defense expense to, its directors 
or other persons, in any such case to a greater extent than is permitted on 
such effective date, the references in this Article to "California law" shall 
to that extent be deemed to refer to California law as so amended."

    Section 29 of the registrant's By-Laws, as amended, provides as follows:

    "29.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

    (a)  INDEMNIFICATION.  To the fullest extent permissible under California 
law, the corporation shall indemnify its directors and officers against all 
expenses, judgment, fines settlement and other amounts actually and 
reasonably incurred by them in connection with any proceeding, including an 
action by or in the right of the corporation, by reason of the fact that such 
person is or was a director or officer of the corporation, or is or was 
serving at the request of the corporation as a director, officer, trustee, 
employee or agent of another corporation, or of a partnership, joint venture, 
trust or other enterprise (including service with respect to employee benefit 
plans).  To the fullest extent permissible under California law, expenses 
incurred by a director or officer seeking indemnification under this By-law 
in defending any proceeding shall be advanced by the corporation as they are 
incurred upon receipt by the corporation of an undertaking by or on behalf of 
the director or officer to repay such amount if it shall ultimately be 
determined that the director or officer is not entitled to be indemnified by 
the corporation for those expenses. If, after the effective date of this 
By-law, California law is amended in a manner which permits the corporation 
to authorize indemnification of or advancement of expenses to its directors 
or officers, in any such case to a greater extent than is permitted on such 
effective date, the references in this By-law to "California law" shall to 
that extent be deemed to refer to California law as so amended.  The rights 
granted by this By-law are contractual in nature and, as such, may not be 
altered with respect to any present or former director or officer without the 
written consent of that person.

    (b)  PROCEDURE.  Upon written request to the Board of Directors by a person
seeking indemnification under this By-law, the Board shall promptly determine in
accordance with Section 317(e) of the California Corporations Code whether the
applicable standard of conduct has been met and, if so, the Board shall
authorize indemnification.  If the Board cannot authorize 

                                  II-3
indemnification because the number of directors who are parties to the 
proceeding with respect to which indemnification is sought prevents the 
formation of a quorum of directors who are not parties to the proceeding, 
then, upon written request by the person seeking indemnification, independent 
legal counsel (by means of a written opinion obtained at the corporation's 
expense) or the corporation's shareholders shall determine whether the 
applicable standard of conduct has been met and, if so, shall authorize 
indemnification.

    (c)  DEFINITIONS.  The term "proceeding" means any threatened, pending or 
completed action or proceeding, whether civil, criminal, administrative or 
investigative.  The term "expenses" includes, without limitation, attorney's 
fees and any expenses of establishing a right to indemnification."

    The registrant has entered into indemnification agreements with each of 
its current directors and officers or persons controlling the Registrant 
pursuant to the foregoing provisions.

ITEM 8.  EXHIBITS

  5.1    Opinion of Heller Ehrman White & McAuliffe

 23.1    Consent of Ernst & Young LLP, Independent Auditors

 23.3    Consent of Heller Ehrman White & McAuliffe
         (filed as part of Exhibit 5.1)

 24.1    Power of Attorney (See page II-6)

 99.1    1993 Stock Plan, as amended

ITEM 9.  UNDERTAKINGS

    A.   The undersigned registrant hereby undertakes:

         (1)  To file, during any period in which offers or sales are being
made, a post-effective amendment to this registration statement;

              (i)  To include any prospectus required by Section 10(a)(3) of
    the Securities Act of 1933, as amended (the "Securities Act");

              (ii) To reflect in the prospectus any facts or events arising
    after the effective date of the registration statement (or the most recent
    post-effective amendment thereof) which, individually or in the aggregate,
    represent a fundamental change in the information set forth in the
    registration statement;

              (iii)    To include any material information with respect to the
    plan of distribution not previously disclosed in the registration statement
    or any material change to such information in the registration statement;

                                  II-4
PROVIDED, HOWEVER, that paragraphs A(1)(i) and A(1)(ii) do not apply if the
information required to be included in a post-effective amendment by those
paragraphs is contained in periodic reports filed by the registrant pursuant to
Section 13 or 15(d) of the Exchange Act that are incorporated by reference in
the registration statement.

         (2)  That, for the purpose of determining any liability under the
Securities Act, each such post-effective amendment shall be deemed to be a new
registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial BONA
FIDE offering thereof.

         (3)  To remove from registration by means of a post-effective
amendment any of the securities being registered which remain unsold at the
termination of the offering.

    B.   The undersigned registrant hereby undertakes that, for purposes of
determining liability under the Securities Act, each filing of the registrant's
annual report pursuant to Section 13(a) or 15(d) of the Exchange Act that is
incorporated by reference in the registration statement shall be deemed a new
registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial BONA
FIDE offering thereof.

    C.   Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the registrant pursuant to the foregoing provisions, or otherwise, the
registrant has been advised that in the opinion of the Securities and Exchange
Commission such indemnification is against public policy as expressed in the
Securities Act and is, therefore, unenforceable.  In the event that a claim for
indemnification against such liabilities (other than the payment by the
registrant of expenses incurred or paid by a director, officer or controlling
person of the registrant in the successful defense of any action, suit or
proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the registrant will, unless in
the opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Securities
Act and will be governed by the final adjudication of such issue.

                                  II-5
SIGNATURES

         Pursuant to the requirements of the Securities Act, 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 Santa Clara, State of California, on this 28th day of
August, 1997.

                                  AFFYMETRIX, INC.

                                  By: /s/ Stephen P.A. Fodor
                                     --------------------------------------
                                     Stephen P.A. Fodor, Ph.D.
                                     President & Chief Executive Officer
                                     (Principal Executive Officer)

                         POWER OF ATTORNEY TO SIGN AMENDMENTS

         KNOW ALL MEN BY THESE PRESENTS, that each person whose signature
appears below does hereby constitute and appoint Stephen P.A. Fodor, Ph.D. and
Edward M. Hurwitz, or either or them, each with full power of substitution, such
person's true and lawful attorneys-in-fact and agents for such person in such
person's name, place and stead, in any and all capacities, to sign any or all
amendments (including post-effective amendments) to this Registration Statement
on Form S-8 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 full power and authority to do and
perform each and every act and thing requisite and necessary to be done in and
about the premises in order to effectuate the same as fully, to all intents and
purposes, as he or such person might or could do in person, hereby ratifying and
confirming all that said attorneys-in-fact and agents may lawfully do or cause
to be done by virtue hereof.

         Pursuant to the requirements of the Securities Act, this Registration
Statement on Form S-8 has been signed by the following persons in the capacities
and on the dates indicated.

                                  II-6
SIGNATURE                       CAPACITY                    DATE     
       ---------                       --------                    ----

/s/ Stephen P.A. Fodor
_____________________________     DIRECTOR, PRESIDENT AND     AUGUST 28, 1997
 STEPHEN P.A. FODOR, PH.D.        CHIEF EXECUTIVE OFFICER
                                  (PRINCIPAL EXECUTIVE 
                                  OFFICER)

_____________________________     DIRECTOR AND CHAIRMAN
    JOHN D. DIEKMAN PH.D.

/s/ Paul Berg
_____________________________     DIRECTOR                    AUGUST 25, 1997
     PAUL BERG, PH.D.

/s/ Douglas M. Hurt
_____________________________     DIRECTOR                    AUGUST 25, 1997
      DOUGLAS M. HURT

/s/ Vernon R. Louks, Jr.
_____________________________     DIRECTOR                    AUGUST 27, 1997
   VERNON R. LOUCKS, JR.

/s/ Barry C. Ross
_____________________________     DIRECTOR                    AUGUST 28, 1997
   BARRY C. ROSS, PH.D.

/s/ David B. Singer
_____________________________     DIRECTOR                    AUGUST 25, 1997
      DAVID B. SINGER

/s/ Lubert Stryer
_____________________________     DIRECTOR                    AUGUST 25, 1997
    LUBERT STRYER, M.D.

/s/ John A. Young
_____________________________     DIRECTOR                    AUGUST 28, 1997
       JOHN A. YOUNG

_____________________________     DIRECTOR
ALEJANDRO C. ZAFFARONI, PH.D.

                                    II-7
/s/ Edward M. Hurwitz
______________________________    VICE PRESIDENT AND          AUGUST 29, 1997
        EDWARD M. HURWITZ         CHIEF FINANCIAL OFFICER
                                  (PRINCIPAL FINANCIAL
                                  OFFICER)

                                    II-8
INDEX TO EXHIBITS

                                                                 Sequentially
 Item                                                              Numbered
  No.                  Description of Item                            Page 
- ------   ------------------------------------------------------  ------------

  5.1    Opinion of Heller Ehrman White & McAuliffe

 23.1    Consent of Ernst & Young LLP, Independent Auditors

 23.3    Consent of Heller Ehrman White & McAuliffe
         (filed as part of Exhibit 5.1)

 24.1    Power of Attorney (see page II-6) 

 99.1    1993 Stock Plan, as amended