<PAGE>

    As filed with the Securities and Exchange Commission on December 27, 2000
                                                     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)

           DELAWARE                                   77-0319159
  (State or other jurisdiction             (IRS Employer of Identification No.)
  Incorporation or organization)

                             3380 CENTRAL EXPRESSWAY
                              SANTA CLARA, CA 95051
               (Address of principal executive offices) (Zip Code)

                                AFFYMETRIX, INC.

                                ----------------

               AFFYMETRIX/NEOMORPHIC, INC. 1998 STOCK OPTION PLAN

                            (Full title of the Plan)

                                -----------------

                                  VERN NORVIEL
         SENIOR VICE PRESIDENT, GENERAL COUNSEL and CORPORATE SECRETARY
                                AFFYMETRIX, INC.
                             3380 CENTRAL EXPRESSWAY
                              SANTA CLARA, CA 95051
                     (Name and address of agent for service)
                                 (408) 731-5000
          (Telephone number, including area code, of agent for service)

                                -----------------

<TABLE>
<CAPTION>
                                                   CALCULATION OF REGISTRATION FEE
==================================================== ==================== =================== =================== ==================
                                                                               PROPOSED            PROPOSED
                                                                               MAXIMUM             MAXIMUM
                                                                               OFFERING           AGGREGATE           AMOUNT OF
           TITLE OF SECURITIES TO BE                    AMOUNT TO BE          PRICE PER            OFFERING         REGISTRATION
                REGISTERED (1)                           REGISTERED           SHARE (2)           PRICE (2)            FEE (2)
---------------------------------------------------- -------------------- ------------------- ------------------- ------------------
<S>                                                  <C>                  <C>                 <C>                 <C>
Common Stock (par value $.01)                              122,757              11.12            1,364,668.20           341.17
==================================================== ==================== =================== =================== ==================
</TABLE>

(1)               This Registration Statement covers shares of Common Stock of
                  Affymetrix, Inc. which may be offered or sold pursuant to the
                  Affymetrix/Neomorphic, Inc. 1998 Stock Option Plan. This
                  Registration Statement shall also cover any additional shares
                  of Common Stock which become issuable under the
                  Affymetrix/Neomorphic, Inc. 1998 Stock Option Plan by reason
                  of any stock dividend, stock split, recapitalization or other
                  similar transaction effected without the receipt of
                  consideration which results in an increase in the number of
                  the outstanding shares of Common Stock of Affymetrix, Inc.

                  This Registration Statement also relates to the Rights to
                  purchase shares of Series B Junior Participating Preferred
                  Stock of Affymetrix, Inc. which are attached to all shares of
                  Common Stock outstanding as of, and issued subsequent to,
                  October 15, 1998, pursuant to Affymetrix, Inc.'s Rights
                  Agreement dated as of October 15, 1998, as amended. Until the
                  occurrence of certain prescribed events, the Rights are not
                  exercisable, are evidenced by the certificates for the Common
                  Stock, and will be transferred with and only with such stock.

(2)               Calculated solely for purposes of this offering under Rule
                  457(h) of the Securities Act of 1933, as amended, based upon
                  the price at which the options may be exercised. The aggregate
                  exercise price for all shares being registered pursuant to
                  this Registration statement is equal to $1,364,668.20 and the
                  maximum offering price for those shares is $11.12.
<PAGE>


                                     PART I

                INFORMATION REQUIRED IN SECTION 10(a) PROSPECTUS

         The information required in Part I of Form S-8 to be contained in a
prospectus meeting the requirements of Section 10(a) of the Securities Act of
1933, as amended (the "Securities Act"), is not required to be filed with the
Securities and Exchange Commission and is omitted from this Registration
Statement in accordance with the explanatory note to Part I of Form S-8 and Rule
428 under the Securities Act.


                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  INCORPORATION OF DOCUMENTS BY REFERENCE

         Affymetrix, Inc. (the "Registrant") hereby incorporates by reference
into this Registration Statement the following documents previously filed with
the Securities and Exchange Commission (the "SEC"):

         -        Annual Report on Form 10-K for the year ended December 31,
                  1999;

         -        Quarterly Reports on Form 10-Q for the quarters ended March
                  31, June 30 and September 30, 2000;

         -        Current Report on Form 8-K filed on February 11, 2000, April
                  7, 2000, April 11, 2000, April 27, 2000, June 13, 2000, July
                  6, 2000, July 21, 2000, August 21, 2000, October 3, 2000,
                  October 20, 2000, November 3, 2000, November 7, 2000, November
                  13, 2000, and November 30, 2000. The Current Report on Form
                  8-K filed on April 7, 2000 includes consolidated financial
                  statements and schedules which reflect the February 2000
                  acquisition of Genetic MicroSystems, Inc. using the pooling
                  of interests method. Such financial statements supercede
                  the consolidated financial statements and schedules
                  included in the Registrant's Annual Report on Form 10-K for
                  the year ended December 31, 1999.

         -        Form 8-A filed on October 16, 1998, as amended by Form 8-A/A
                  filed on March 29, 2000; and

         -        Registration Statement No. 0-28218 on Form 8-A filed with the
                  SEC on April 16, 1996 pursuant to Section 10 of the Securities
                  Exchange Act of 1934, as amended, with amendments thereto, in
                  which there is described the terms, rights and provisions
                  applicable to the Registrant's Common Stock.

         All reports and definitive proxy or information statements filed
pursuant to Section 13(a), 13(c), 14 or 15(d) of the 1934 Act after the date of
this Registration Statement and 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 shall be deemed to be
incorporated by reference into this Registration Statement and to be a part
hereof from the date of filing of such documents.

Item 4.  DESCRIPTION OF SECURITIES

         Not Applicable.

Item 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL

         The legality of the shares of Common Stock offered hereby has been
passed upon for the Registrant by Vern Norviel, Esq. Mr. Norviel is Senior
Vice President, General Counsel and Corporate Secretary of Affymetrix, Inc.

<PAGE>

Item 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

         Section 145 of the Delaware General Corporation law empowers a Delaware
corporation to indemnify any person who is, or is threatened to be made, a party
to any threatened, pending or completed legal action, suit or proceedings,
whether civil, criminal, administrative or investigative (other than by or in
the right of such corporation), by reason of the fact that such person is or was
an officer or director of such corporation, or is or was serving at the request
of such corporation as a director, officer, employee or agent of another
corporation or enterprise. The indemnity may include expenses (including
attorneys' fees), judgements, fines and amounts paid in settlement actually and
reasonably incurred by such person in connection with such action, suit or
proceeding, provided that such person acted in good faith and in a manner he or
she reasonably believed to be in or not opposed to the corporation's best
interests, and, for criminal proceedings, had no reasonable cause to believe his
or her conduct was illegal. A Delaware corporation may indemnify officers and
directors in an action by or in the right of the corporation under the same
conditions, except that no indemnification is permitted without judicial
approval if the officer or director is adjudged to be liable to the corporation
in the performance of his duty. Where an officer or director is successful on
the merits or otherwise in the defense of any action referred to above, the
corporation must indemnify him or her against the expenses which such officer or
director actually and reasonably incurred.

         In accordance with Delaware law, Registrant's restated certificate of
incorporation contains a provision to limit the personal liability of
Registrant's directors for violations of their fiduciary duty as a director.
This provision eliminates each director's liability to Registrant or
Registrant's stockholders for monetary damages except (i) for any breach of the
director's duty of loyalty to Registrant or Registrant's stockholders, (ii) for
acts or omissions not in good faith or which involve intentional misconduct or a
knowing violation of law, (iii) under Section 174 of the Delaware General
Corporation law providing for liability of directors for unlawful payment of
dividends or unlawful stock purchases or redemptions, or (iv) for any
transaction from which a director derived an improper personal benefit. The
effect of this provision is to eliminate the personal liability of directors for
monetary damages for actions involving a breach of their fiduciary duty of care,
including any such actions involving gross negligence.

         Registrant's restated certificate of incorporation and bylaws provide
for indemnification of its officers and directors to the fullest extent
permitted by applicable law.

         Registrant has entered into indemnification agreements with each
director and executive officer which provide indemnification to such directors
and executive officers under certain circumstances for acts or omissions which
may not be covered by directors' and officers' liability insurance.

Item 7.  EXEMPTION FROM REGISTRATION CLAIMED

         Not Applicable.

Item 8.   EXHIBITS

<TABLE>
<CAPTION>
         Exhibit Number             Exhibit
         --------------             -------
        <S>                        <C>
              (1)4.1                Restated Certificate of
                                    Incorporation of Affymetrix, Inc.

              (2)4.2                Bylaws of Affymetrix, Inc.

              (3)4.3                Rights Agreement, dated as of October 15,
                                    1998,


<PAGE>

                                    between Affymetrix, Inc. and American Stock
                                    Transfer & Trust Company, as Rights Agent

              (4)4.4                Amendment No. 1 to Rights Agreement, dated
                                    as of February 7, 2000, between Affymetrix,
                                    Inc. and American Stock Transfer & Trust
                                    Company, as Rights Agent

                5.1                 Opinion of Vern Norviel, Esq., Senior Vice
                                    President, General Counsel, and Corporate
                                    Secretary

               23.1                 Consent of Ernst & Young LLP, Independent
                                    Auditors

               23.2                 Consent of Vern Norviel, Esq. (included in
                                    Exhibit 5.1)

               24.1                 Power of Attorney (included on the signature
                                    page hereto)

               99.1                 Neomorphic Software, Inc. 1998 Stock Option
                                    Plan (5)

               99.2                 First Amendment to Neomorphic Software, Inc.
                                    1998 Stock Option Plan

               99.3                 Second Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan

               99.4                 Third Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan
</TABLE>


(1)      Incorporated by reference to Exhibit 3.1 to our Form 8-K as filed on
         June 13, 2000 (File No. 000-28218).

(2)      Incorporated by reference to Appendix C to our definitive proxy
         statement on Schedule 14A as filed on April 29, 1998 (File No.
         000-28218).

(3)      Incorporated by reference to Exhibit 1 of our Form 8-A as filed on
         October 16, 1998 (File No. 000-28218).

(4)      Incorporated by reference to Exhibit 4.1 of our Form 8-A/A as filed on
         March 29, 2000 (File No. 000-28218).

(5)      Neomorphic Software, Inc. changed its name to Neomorphic, Inc. on
         January 27, 2000.

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 1933 Act, (ii) to reflect in the prospectus any facts or events
arising after the effective date of this 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 this
Registration Statement and (iii) to include any material information with
respect to the plan of distribution not previously disclosed in this
Registration Statement or any material change to such information in this
Registration Statement; provided, however, that clauses (1)(i) and (1)(ii) shall
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 Section 15(d) of the 1934 Act that are
incorporated by reference into this Registration Statement; (2) that for the
<PAGE>

purpose of determining any liability under the 1933 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; and (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
Affymetrix/Neomorphic 1998 Stock Option Plan.

         B. The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the 1933 Act, each filing of the Registrant's
annual report pursuant to Section 13(a) or Section 15(d) of the 1934 Act that is
incorporated by reference into this Registration Statement 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.

         C. Insofar as indemnification for liabilities arising under the 1933
Act may be permitted to directors, officers or controlling persons of the
Registrant pursuant to the indemnification provisions summarized in Item 6 or
otherwise, the Registrant has been advised that, in the opinion of the SEC, such
indemnification is against public policy as expressed in the 1933 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 1933 Act and will be governed by the final
adjudication of such issue.


<PAGE>



                                   SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, as amended,
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 27th
day of December, 2000.

                                        AFFYMETRIX,  INC.


                                        By:    /s/ Vern Norviel
                                               ---------------------------------
                                               Vern Norviel
                                               Senior Vice President, General
                                               Counsel and Corporate Secretary

                                POWER OF ATTORNEY


KNOW ALL PERSONS BY THESE PRESENTS:

         That the undersigned officers and directors of Affymetrix, Inc., a
Delaware corporation, do hereby constitute and appoint Stephen P.A. Fodor and
Vern Norviel, and either of them, the lawful attorneys-in-fact and agents with
full power and authority to do any and all acts and things and to execute any
and all instruments which said attorneys and agents, and either one of them,
determine may be necessary or advisable or required to enable said corporation
to comply with the Securities Act of 1933, as amended, and any rules or
regulations or requirements of the Securities and Exchange Commission in
connection with this Registration Statement. Without limiting the generality of
the foregoing power and authority, the powers granted include the power and
authority to sign the names of the undersigned officers and directors in the
capacities indicated below to this Registration Statement, to any and all
amendments, both pre-effective and post-effective, and supplements to this
Registration Statement, and to any and all instruments or documents filed as
part of or in conjunction with this Registration Statement or amendments or
supplements thereof, and either of the undersigned hereby ratifies and confirms
all that said attorneys and agents, or either one of them, shall do or cause to
be done by virtue hereof. This Power of Attorney may be signed in several
counterparts.

         IN WITNESS WHEREOF, each of the undersigned has executed this Power of
Attorney as of the date indicated.

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

<TABLE>
<CAPTION>
Signature                                                   Title                                  Date
---------                                                   -----                                  ----

<S>                                             <C>                                         <C>
/s/ Stephen P.A. Fodor                           Chief Executive Officer and                 December 27, 2000
------------------------------------                 Chairman of the Board
Stephen P.A. Fodor, Ph.D.


/s/ Edward M. Hurwitz                          Senior Vice President and Chief               December 27, 2000
------------------------------------            Financial Officer (Principal
Edward M. Hurwitz                                 Financial and Accounting
                                                           Officer)


/s/ John D. Diekman                                       Director                           December 27, 2000
------------------------------------
John D. Diekman, Ph.D.


                                                          Director
------------------------------------
Paul Berg, Ph.D.


/s/ Vernon R. Loucks, Jr.                                 Director                           December 27, 2000
------------------------------------
Vernon R. Loucks, Jr.


/s/ David B. Singer                                       Director                           December 27, 2000
------------------------------------
David B. Singer


                                                          Director
------------------------------------
Lubert Stryer, M.D.


/s/ John A. Young                                         Director                           December 27, 2000
------------------------------------
John A. Young
</TABLE>





<PAGE>



                                  EXHIBIT INDEX


<TABLE>
<CAPTION>
         Exhibit Number             Exhibit
         --------------             -------
        <S>                        <C>
              (1)4.1                Restated Certificate of Incorporation of
                                    Affymetrix, Inc.

              (2)4.2                Bylaws of Affymetrix, Inc.

              (3)4.3                Rights Agreement, dated as of October 15,
                                    1998, between Affymetrix, Inc. and American
                                    Stock Transfer & Trust Company, as Rights
                                    Agent

              (4)4.4                Amendment No. 1 to Rights Agreement, dated
                                    as of February 7, 2000, between Affymetrix,
                                    Inc. and American Stock Transfer & Trust
                                    Company, as Rights Agent

                5.1                 Opinion of Vern Norviel, Esq., Senior Vice
                                    President, General Counsel, and Corporate
                                    Secretary

               23.1                 Consent of Ernst & Young LLP, Independent
                                    Auditors

               23.2                 Consent of Vern Norviel, Esq. (included in
                                    Exhibit 5.1)

               24.1                 Power of Attorney (included on the signature
                                    page hereto)

               99.1                 Neomorphic Software, Inc. 1998 Stock Option
                                    Plan

               99.2                 First Amendment to Neomorphic Software, Inc.
                                    1998 Stock Option Plan

               99.3                 Second Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan

               99.4                 Third Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan
</TABLE>


(1)     Incorporated by reference to Exhibit 3.1 to our Form 8-K as filed on
        June 13, 2000 (File No. 000-28218).

(2)     Incorporated by reference to Appendix C to our definitive proxy
        statement on Schedule 14A as filed on April 29, 1998 (File No.
        000-28218).

(3)     Incorporated by reference to Exhibit 1 of our Form 8-A as filed on
        October 16, 1998 (File No. 000-28218).

(4)     Incorporated by reference to Exhibit 4.1 of our Form 8-A/A as filed on
        March 29, 2000 (File No. 000-28218).
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{"company-data": {"conformed-name": "AFFYMETRIX INC", "cik": "0000913077", "assigned-sic": "8731", "irs-number": "770319159", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-52804", "film-number": "796406"}, "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 December 27, 2000
                                                     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)

           DELAWARE                                   77-0319159
  (State or other jurisdiction             (IRS Employer of Identification No.)
  Incorporation or organization)

                             3380 CENTRAL EXPRESSWAY
                              SANTA CLARA, CA 95051
               (Address of principal executive offices) (Zip Code)

                                AFFYMETRIX, INC.

                                ----------------

               AFFYMETRIX/NEOMORPHIC, INC. 1998 STOCK OPTION PLAN

                            (Full title of the Plan)

                                -----------------

                                  VERN NORVIEL
         SENIOR VICE PRESIDENT, GENERAL COUNSEL and CORPORATE SECRETARY
                                AFFYMETRIX, INC.
                             3380 CENTRAL EXPRESSWAY
                              SANTA CLARA, CA 95051
                     (Name and address of agent for service)
                                 (408) 731-5000
          (Telephone number, including area code, of agent for service)

                                -----------------
CALCULATION OF REGISTRATION FEE
==================================================== ==================== =================== =================== ==================
                                                                               PROPOSED            PROPOSED
                                                                               MAXIMUM             MAXIMUM
                                                                               OFFERING           AGGREGATE           AMOUNT OF
           TITLE OF SECURITIES TO BE                    AMOUNT TO BE          PRICE PER            OFFERING         REGISTRATION
                REGISTERED (1)                           REGISTERED           SHARE (2)           PRICE (2)            FEE (2)
---------------------------------------------------- -------------------- ------------------- ------------------- ------------------
Common Stock (par value $.01)                              122,757              11.12            1,364,668.20           341.17
==================================================== ==================== =================== =================== ==================
(1)               This Registration Statement covers shares of Common Stock of
                  Affymetrix, Inc. which may be offered or sold pursuant to the
                  Affymetrix/Neomorphic, Inc. 1998 Stock Option Plan. This
                  Registration Statement shall also cover any additional shares
                  of Common Stock which become issuable under the
                  Affymetrix/Neomorphic, Inc. 1998 Stock Option Plan by reason
                  of any stock dividend, stock split, recapitalization or other
                  similar transaction effected without the receipt of
                  consideration which results in an increase in the number of
                  the outstanding shares of Common Stock of Affymetrix, Inc.

                  This Registration Statement also relates to the Rights to
                  purchase shares of Series B Junior Participating Preferred
                  Stock of Affymetrix, Inc. which are attached to all shares of
                  Common Stock outstanding as of, and issued subsequent to,
                  October 15, 1998, pursuant to Affymetrix, Inc.'s Rights
                  Agreement dated as of October 15, 1998, as amended. Until the
                  occurrence of certain prescribed events, the Rights are not
                  exercisable, are evidenced by the certificates for the Common
                  Stock, and will be transferred with and only with such stock.

(2)               Calculated solely for purposes of this offering under Rule
                  457(h) of the Securities Act of 1933, as amended, based upon
                  the price at which the options may be exercised. The aggregate
                  exercise price for all shares being registered pursuant to
                  this Registration statement is equal to $1,364,668.20 and the
                  maximum offering price for those shares is $11.12.
PART I

                INFORMATION REQUIRED IN SECTION 10(a) PROSPECTUS

         The information required in Part I of Form S-8 to be contained in a
prospectus meeting the requirements of Section 10(a) of the Securities Act of
1933, as amended (the "Securities Act"), is not required to be filed with the
Securities and Exchange Commission and is omitted from this Registration
Statement in accordance with the explanatory note to Part I of Form S-8 and Rule
428 under the Securities Act.

                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  INCORPORATION OF DOCUMENTS BY REFERENCE

         Affymetrix, Inc. (the "Registrant") hereby incorporates by reference
into this Registration Statement the following documents previously filed with
the Securities and Exchange Commission (the "SEC"):

         -        Annual Report on Form 10-K for the year ended December 31,
                  1999;

         -        Quarterly Reports on Form 10-Q for the quarters ended March
                  31, June 30 and September 30, 2000;

         -        Current Report on Form 8-K filed on February 11, 2000, April
                  7, 2000, April 11, 2000, April 27, 2000, June 13, 2000, July
                  6, 2000, July 21, 2000, August 21, 2000, October 3, 2000,
                  October 20, 2000, November 3, 2000, November 7, 2000, November
                  13, 2000, and November 30, 2000. The Current Report on Form
                  8-K filed on April 7, 2000 includes consolidated financial
                  statements and schedules which reflect the February 2000
                  acquisition of Genetic MicroSystems, Inc. using the pooling
                  of interests method. Such financial statements supercede
                  the consolidated financial statements and schedules
                  included in the Registrant's Annual Report on Form 10-K for
                  the year ended December 31, 1999.

         -        Form 8-A filed on October 16, 1998, as amended by Form 8-A/A
                  filed on March 29, 2000; and

         -        Registration Statement No. 0-28218 on Form 8-A filed with the
                  SEC on April 16, 1996 pursuant to Section 10 of the Securities
                  Exchange Act of 1934, as amended, with amendments thereto, in
                  which there is described the terms, rights and provisions
                  applicable to the Registrant's Common Stock.

         All reports and definitive proxy or information statements filed
pursuant to Section 13(a), 13(c), 14 or 15(d) of the 1934 Act after the date of
this Registration Statement and 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 shall be deemed to be
incorporated by reference into this Registration Statement and to be a part
hereof from the date of filing of such documents.

Item 4.  DESCRIPTION OF SECURITIES

         Not Applicable.

Item 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL

         The legality of the shares of Common Stock offered hereby has been
passed upon for the Registrant by Vern Norviel, Esq. Mr. Norviel is Senior
Vice President, General Counsel and Corporate Secretary of Affymetrix, Inc.
Item 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS

         Section 145 of the Delaware General Corporation law empowers a Delaware
corporation to indemnify any person who is, or is threatened to be made, a party
to any threatened, pending or completed legal action, suit or proceedings,
whether civil, criminal, administrative or investigative (other than by or in
the right of such corporation), by reason of the fact that such person is or was
an officer or director of such corporation, or is or was serving at the request
of such corporation as a director, officer, employee or agent of another
corporation or enterprise. The indemnity may include expenses (including
attorneys' fees), judgements, fines and amounts paid in settlement actually and
reasonably incurred by such person in connection with such action, suit or
proceeding, provided that such person acted in good faith and in a manner he or
she reasonably believed to be in or not opposed to the corporation's best
interests, and, for criminal proceedings, had no reasonable cause to believe his
or her conduct was illegal. A Delaware corporation may indemnify officers and
directors in an action by or in the right of the corporation under the same
conditions, except that no indemnification is permitted without judicial
approval if the officer or director is adjudged to be liable to the corporation
in the performance of his duty. Where an officer or director is successful on
the merits or otherwise in the defense of any action referred to above, the
corporation must indemnify him or her against the expenses which such officer or
director actually and reasonably incurred.

         In accordance with Delaware law, Registrant's restated certificate of
incorporation contains a provision to limit the personal liability of
Registrant's directors for violations of their fiduciary duty as a director.
This provision eliminates each director's liability to Registrant or
Registrant's stockholders for monetary damages except (i) for any breach of the
director's duty of loyalty to Registrant or Registrant's stockholders, (ii) for
acts or omissions not in good faith or which involve intentional misconduct or a
knowing violation of law, (iii) under Section 174 of the Delaware General
Corporation law providing for liability of directors for unlawful payment of
dividends or unlawful stock purchases or redemptions, or (iv) for any
transaction from which a director derived an improper personal benefit. The
effect of this provision is to eliminate the personal liability of directors for
monetary damages for actions involving a breach of their fiduciary duty of care,
including any such actions involving gross negligence.

         Registrant's restated certificate of incorporation and bylaws provide
for indemnification of its officers and directors to the fullest extent
permitted by applicable law.

         Registrant has entered into indemnification agreements with each
director and executive officer which provide indemnification to such directors
and executive officers under certain circumstances for acts or omissions which
may not be covered by directors' and officers' liability insurance.

Item 7.  EXEMPTION FROM REGISTRATION CLAIMED

         Not Applicable.

Item 8.   EXHIBITS
Exhibit Number             Exhibit
         --------------             -------
(1)4.1                Restated Certificate of
                                    Incorporation of Affymetrix, Inc.

              (2)4.2                Bylaws of Affymetrix, Inc.

              (3)4.3                Rights Agreement, dated as of October 15,
                                    1998,
between Affymetrix, Inc. and American Stock
                                    Transfer & Trust Company, as Rights Agent

              (4)4.4                Amendment No. 1 to Rights Agreement, dated
                                    as of February 7, 2000, between Affymetrix,
                                    Inc. and American Stock Transfer & Trust
                                    Company, as Rights Agent

                5.1                 Opinion of Vern Norviel, Esq., Senior Vice
                                    President, General Counsel, and Corporate
                                    Secretary

               23.1                 Consent of Ernst & Young LLP, Independent
                                    Auditors

               23.2                 Consent of Vern Norviel, Esq. (included in
                                    Exhibit 5.1)

               24.1                 Power of Attorney (included on the signature
                                    page hereto)

               99.1                 Neomorphic Software, Inc. 1998 Stock Option
                                    Plan (5)

               99.2                 First Amendment to Neomorphic Software, Inc.
                                    1998 Stock Option Plan

               99.3                 Second Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan

               99.4                 Third Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan
(1)      Incorporated by reference to Exhibit 3.1 to our Form 8-K as filed on
         June 13, 2000 (File No. 000-28218).

(2)      Incorporated by reference to Appendix C to our definitive proxy
         statement on Schedule 14A as filed on April 29, 1998 (File No.
         000-28218).

(3)      Incorporated by reference to Exhibit 1 of our Form 8-A as filed on
         October 16, 1998 (File No. 000-28218).

(4)      Incorporated by reference to Exhibit 4.1 of our Form 8-A/A as filed on
         March 29, 2000 (File No. 000-28218).

(5)      Neomorphic Software, Inc. changed its name to Neomorphic, Inc. on
         January 27, 2000.

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 1933 Act, (ii) to reflect in the prospectus any facts or events
arising after the effective date of this 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 this
Registration Statement and (iii) to include any material information with
respect to the plan of distribution not previously disclosed in this
Registration Statement or any material change to such information in this
Registration Statement; provided, however, that clauses (1)(i) and (1)(ii) shall
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 Section 15(d) of the 1934 Act that are
incorporated by reference into this Registration Statement; (2) that for the
purpose of determining any liability under the 1933 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; and (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
Affymetrix/Neomorphic 1998 Stock Option Plan.

         B. The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the 1933 Act, each filing of the Registrant's
annual report pursuant to Section 13(a) or Section 15(d) of the 1934 Act that is
incorporated by reference into this Registration Statement 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.

         C. Insofar as indemnification for liabilities arising under the 1933
Act may be permitted to directors, officers or controlling persons of the
Registrant pursuant to the indemnification provisions summarized in Item 6 or
otherwise, the Registrant has been advised that, in the opinion of the SEC, such
indemnification is against public policy as expressed in the 1933 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 1933 Act and will be governed by the final
adjudication of such issue.
SIGNATURES

         Pursuant to the requirements of the Securities Act of 1933, as amended,
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 27th
day of December, 2000.

                                        AFFYMETRIX,  INC.

                                        By:    /s/ Vern Norviel
                                               ---------------------------------
                                               Vern Norviel
                                               Senior Vice President, General
                                               Counsel and Corporate Secretary

                                POWER OF ATTORNEY

KNOW ALL PERSONS BY THESE PRESENTS:

         That the undersigned officers and directors of Affymetrix, Inc., a
Delaware corporation, do hereby constitute and appoint Stephen P.A. Fodor and
Vern Norviel, and either of them, the lawful attorneys-in-fact and agents with
full power and authority to do any and all acts and things and to execute any
and all instruments which said attorneys and agents, and either one of them,
determine may be necessary or advisable or required to enable said corporation
to comply with the Securities Act of 1933, as amended, and any rules or
regulations or requirements of the Securities and Exchange Commission in
connection with this Registration Statement. Without limiting the generality of
the foregoing power and authority, the powers granted include the power and
authority to sign the names of the undersigned officers and directors in the
capacities indicated below to this Registration Statement, to any and all
amendments, both pre-effective and post-effective, and supplements to this
Registration Statement, and to any and all instruments or documents filed as
part of or in conjunction with this Registration Statement or amendments or
supplements thereof, and either of the undersigned hereby ratifies and confirms
all that said attorneys and agents, or either one of them, shall do or cause to
be done by virtue hereof. This Power of Attorney may be signed in several
counterparts.

         IN WITNESS WHEREOF, each of the undersigned has executed this Power of
Attorney as of the date indicated.

         Pursuant to the requirements of the Securities Act of 1933, as amended,
this Registration Statement has been signed below by the following persons in
the capacities and on the dates indicated.
Signature                                                   Title                                  Date
---------                                                   -----                                  ----
/s/ Stephen P.A. Fodor                           Chief Executive Officer and                 December 27, 2000
------------------------------------                 Chairman of the Board
Stephen P.A. Fodor, Ph.D.

/s/ Edward M. Hurwitz                          Senior Vice President and Chief               December 27, 2000
------------------------------------            Financial Officer (Principal
Edward M. Hurwitz                                 Financial and Accounting
                                                           Officer)

/s/ John D. Diekman                                       Director                           December 27, 2000
------------------------------------
John D. Diekman, Ph.D.

                                                          Director
------------------------------------
Paul Berg, Ph.D.

/s/ Vernon R. Loucks, Jr.                                 Director                           December 27, 2000
------------------------------------
Vernon R. Loucks, Jr.

/s/ David B. Singer                                       Director                           December 27, 2000
------------------------------------
David B. Singer

                                                          Director
------------------------------------
Lubert Stryer, M.D.

/s/ John A. Young                                         Director                           December 27, 2000
------------------------------------
John A. Young
EXHIBIT INDEX
Exhibit Number             Exhibit
         --------------             -------
(1)4.1                Restated Certificate of Incorporation of
                                    Affymetrix, Inc.

              (2)4.2                Bylaws of Affymetrix, Inc.

              (3)4.3                Rights Agreement, dated as of October 15,
                                    1998, between Affymetrix, Inc. and American
                                    Stock Transfer & Trust Company, as Rights
                                    Agent

              (4)4.4                Amendment No. 1 to Rights Agreement, dated
                                    as of February 7, 2000, between Affymetrix,
                                    Inc. and American Stock Transfer & Trust
                                    Company, as Rights Agent

                5.1                 Opinion of Vern Norviel, Esq., Senior Vice
                                    President, General Counsel, and Corporate
                                    Secretary

               23.1                 Consent of Ernst & Young LLP, Independent
                                    Auditors

               23.2                 Consent of Vern Norviel, Esq. (included in
                                    Exhibit 5.1)

               24.1                 Power of Attorney (included on the signature
                                    page hereto)

               99.1                 Neomorphic Software, Inc. 1998 Stock Option
                                    Plan

               99.2                 First Amendment to Neomorphic Software, Inc.
                                    1998 Stock Option Plan

               99.3                 Second Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan

               99.4                 Third Amendment to Neomorphic, Inc. 1998
                                    Stock Option Plan
(1)     Incorporated by reference to Exhibit 3.1 to our Form 8-K as filed on
        June 13, 2000 (File No. 000-28218).

(2)     Incorporated by reference to Appendix C to our definitive proxy
        statement on Schedule 14A as filed on April 29, 1998 (File No.
        000-28218).

(3)     Incorporated by reference to Exhibit 1 of our Form 8-A as filed on
        October 16, 1998 (File No. 000-28218).

(4)     Incorporated by reference to Exhibit 4.1 of our Form 8-A/A as filed on
        March 29, 2000 (File No. 000-28218).