<PAGE>







      As filed with the Securities and Exchange Commission on September 3, 1996
                                      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
                     1996 Nonemployee Directors Stock Option Plan
                               (Full Title of the Plan)

                                Kenneth J. Nussbacher
                 Executive Vice President and Chief Financial Officer
                                   Affymetrix, Inc.
                3380 CENTRAL EXPRESSWAY, SANTA CLARA, CALIFORNIA 95051
               ------------------------------------------------------
                       (Name and Address of Agent For Service)

                                   (408) 522-6000
         --------------------------------------------------------------
            (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 Maximum     Proposed Maximum         Amount of
Title of Securities            Amount to be       Offering Price     Aggregate Offering       Registration
to be Registered                Registered         per Share (1)            Price                 Fee
- -----------------------------------------------------------------------------------------------------------
<S>                             <C>               <C>                 <C>                      <C>
Common Stock, no par value      3,394,521            $13.875              $47,098,978            $16,242
- -----------------------------------------------------------------------------------------------------------
- -----------------------------------------------------------------------------------------------------------
</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 August 30, 1996.

<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 Quarterly Report on Form 10-Q for the fiscal
quarter ended June 30, 1996;

         (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
beneficially own 27,080 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 law, to indemnify its agents (as defined in Section 317 of the
California Corporations Code), whether by by-law, agreement or


                                         II-2

<PAGE>

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 indemnification
because the number of directors who are parties to the proceeding with respect
to which indemnification is sought


                                         II-3

<PAGE>

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       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)

 24      Power of Attorney (See page II-6)

 99.1    1993 Stock Plan, as amended

 99.2    1996 Nonemployee Directors Stock Option Plan


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


                                         II-4

<PAGE>

    in the registration statement or any material change to such information in
    the registration statement;

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 30th day of
August, 1996.

                                                AFFYMETRIX, INC.



                                                By: /s/ John D. Diekman
                                                   --------------------------
                                                   John D. Diekman, Ph.D.
                                                   Chief Executive Officer and
                                                   Chairman
                                                  (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 John D. Diekman, Ph.D. and
Kenneth J. Nussbacher, 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/ John D. Diekman
    ---------------------------
    John D. Diekman Ph.D.              Director, Chief          August 30, 1996
                                       Executive Officer and
                                       Chairman
                                       (Principal Executive
                                       Officer)
    /s/ Stephen P.A. Fodor
    ---------------------------
    Stephen P.A. Fodor, Ph.D.          Director and President   August 30, 1996
                               
    /s/ Paul Berg
    ---------------------------
    Paul Berg, Ph.D.                   Director                 August 30, 1996
                                                       
    /s/ Douglas M. Hurt
    ---------------------------
    Douglas M. Hurt                    Director                 August 30, 1996
                                                                      
    /s/ Vernon R. Loucks, Jr.
    ---------------------------
    Vernon R. Loucks, Jr.              Director                 August 30, 1996
                                                                    
    /s/ Barry C. Ross
    ---------------------------
    Barry C. Ross, Ph.D.               Director                 August 30, 1996
                                                                     
    /s/ David B. Singer
    ---------------------------
    David B. Singer                    Director                 August 30, 1996
                                                                   
    /s/ John A. Young
    ---------------------------
    John A. Young                      Director                 August 30, 1996
                                                                    

    ----------------------------
    Alejandro C. Zaffaroni, Ph.D.      Director
                                                                   
    /s/ Kenneth J. Nussbacher
    ----------------------------
    Kenneth J. Nussbacher              Chief Financial          August 30, 1996
                                       Officer (Principal            
                                       Financial and
                                       Accounting Officer)


                                         II-7

<PAGE>

                                  INDEX TO EXHIBITS
                                 ------------------



                                                                   SEQUENTIALLY
  ITEM                                                               NUMBERED
   NO.            DESCRIPTION OF ITEM                                  PAGE
  ----  -------------------------------------------------------    ------------
   5         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). . . . . . . . . . . . .

  24         Power of Attorney (see page II-6) . . . . . . . . . .

  99.1       1993 Stock Plan, as amended . . . . . . . . . . . . .

  99.2       1996 Nonemployee Directors Stock Option Plan. . . . .
[{"type": "S-8", "sequence": "1", "description": "FORM S-8", "secsgml_size_bytes": 19823}]
{"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", "act": "33", "file-number": "333-11299", "film-number": "96625065"}, "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 3, 1996
                                      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
                     1996 Nonemployee Directors Stock Option Plan
                               (Full Title of the Plan)

                                Kenneth J. Nussbacher
                 Executive Vice President and Chief Financial Officer
                                   Affymetrix, Inc.
                3380 CENTRAL EXPRESSWAY, SANTA CLARA, CALIFORNIA 95051
               ------------------------------------------------------
                       (Name and Address of Agent For Service)

                                   (408) 522-6000
         --------------------------------------------------------------
            (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 Maximum     Proposed Maximum         Amount of
Title of Securities            Amount to be       Offering Price     Aggregate Offering       Registration
to be Registered                Registered         per Share (1)            Price                 Fee
- -----------------------------------------------------------------------------------------------------------
Common Stock, no par value      3,394,521            $13.875              $47,098,978            $16,242
- -----------------------------------------------------------------------------------------------------------
- -----------------------------------------------------------------------------------------------------------
(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 August 30, 1996.
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 Quarterly Report on Form 10-Q for the fiscal
quarter ended June 30, 1996;

         (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
beneficially own 27,080 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 law, to indemnify its agents (as defined in Section 317 of the
California Corporations Code), whether by by-law, agreement or

                                         II-2
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 indemnification
because the number of directors who are parties to the proceeding with respect
to which indemnification is sought

                                         II-3
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       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)

 24      Power of Attorney (See page II-6)

 99.1    1993 Stock Plan, as amended

 99.2    1996 Nonemployee Directors Stock Option Plan

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

                                         II-4
in the registration statement or any material change to such information in
    the registration statement;

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 30th day of
August, 1996.

                                                AFFYMETRIX, INC.

                                                By: /s/ John D. Diekman
                                                   --------------------------
                                                   John D. Diekman, Ph.D.
                                                   Chief Executive Officer and
                                                   Chairman
                                                  (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 John D. Diekman, Ph.D. and
Kenneth J. Nussbacher, 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/ John D. Diekman
    ---------------------------
    John D. Diekman Ph.D.              Director, Chief          August 30, 1996
                                       Executive Officer and
                                       Chairman
                                       (Principal Executive
                                       Officer)
    /s/ Stephen P.A. Fodor
    ---------------------------
    Stephen P.A. Fodor, Ph.D.          Director and President   August 30, 1996
                               
    /s/ Paul Berg
    ---------------------------
    Paul Berg, Ph.D.                   Director                 August 30, 1996
                                                       
    /s/ Douglas M. Hurt
    ---------------------------
    Douglas M. Hurt                    Director                 August 30, 1996
                                                                      
    /s/ Vernon R. Loucks, Jr.
    ---------------------------
    Vernon R. Loucks, Jr.              Director                 August 30, 1996
                                                                    
    /s/ Barry C. Ross
    ---------------------------
    Barry C. Ross, Ph.D.               Director                 August 30, 1996
                                                                     
    /s/ David B. Singer
    ---------------------------
    David B. Singer                    Director                 August 30, 1996
                                                                   
    /s/ John A. Young
    ---------------------------
    John A. Young                      Director                 August 30, 1996
                                                                    

    ----------------------------
    Alejandro C. Zaffaroni, Ph.D.      Director
                                                                   
    /s/ Kenneth J. Nussbacher
    ----------------------------
    Kenneth J. Nussbacher              Chief Financial          August 30, 1996
                                       Officer (Principal            
                                       Financial and
                                       Accounting Officer)

                                         II-7
INDEX TO EXHIBITS
                                 ------------------

                                                                   SEQUENTIALLY
  ITEM                                                               NUMBERED
   NO.            DESCRIPTION OF ITEM                                  PAGE
  ----  -------------------------------------------------------    ------------
   5         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). . . . . . . . . . . . .

  24         Power of Attorney (see page II-6) . . . . . . . . . .

  99.1       1993 Stock Plan, as amended . . . . . . . . . . . . .

  99.2       1996 Nonemployee Directors Stock Option Plan. . . . .