July 10, 2000



Affymetrix, Inc.,
  3380 Central Expressway,
    Santa Clara, California 95051.

Dear Sirs:

                  In connection with the registration under the Securities
Act of 1933 (the "Act") of $225,000,000 principal amount of 4 3/4%
Convertible Subordinated Notes Due 2007 (the "Securities") of Affymetrix,
Inc., a Delaware corporation (the "Company"), the shares of Common Stock, par
value $0.01 per share, of the Company initially issuable upon conversion of
the Securities (the "Shares") and the rights related to the Shares (the
"Rights") to purchase shares of Series B Junior Participating Preferred Stock
of the Company to be issued pursuant to the Rights Agreement, dated as of
October 15, 1998, between the Company and American Stock Transfer & Trust
Company, as rights agent (the "Rights Agent"), as amended on February 7, 2000
(the "Rights Agreement"), we, as your counsel, have examined such corporate
records, certificates and other documents, and such questions of law, as we
have considered necessary or appropriate for the purposes of this opinion.
Upon the basis of such examination, we advise you that, in our opinion:



Affymetrix, Inc.

                                                                           -2-



                  (1) When the registration statement relating to the
         Securities, the Shares and the Rights (the "Registration Statement")
         has become effective under the Act, the Securities will constitute
         valid and legally binding obligations of the Company, subject to
         bankruptcy, insolvency, fraudulent transfer, reorganization,
         moratorium and similar laws of general applicability relating to or
         affecting creditors' rights and to general equity principles, and
         the Shares, when duly issued upon conversion of the Securities, will
         be validly issued, fully paid and nonassessable.

                  (2) Assuming that the Board of Directors of the Company,
         after fully informing itself with respect to the Rights Agreement
         and the Rights and after giving due consideration to all relevant
         matters, determined that the execution and delivery of the Rights
         Agreement and the issuance of the Rights thereunder would be in the
         best interests of the Company and its stockholders, and assuming
         further that the Rights Agreement has been duly authorized, executed
         and delivered by the Rights Agent, then, when the Registration
         Statement has become effective under the Act and the Shares have been


Affymetrix, Inc.

                                                                           -3-


         validly issued upon conversion of the Securities, the Rights
         attributable to the Shares will be validly issued.

                  In connection with our opinion set forth in paragraph (2)
above, we note that the question whether the Board of Directors of the
Company might be required to redeem the Rights at some future time will
depend upon the facts and circumstances existing at that time and,
accordingly, is beyond the scope of such opinion.

                  The foregoing opinion is limited to the Federal laws of the
United States, the laws of the State of New York and the General Corporation
Law of the State of Delaware, and we are expressing no opinion as to the
effect of the laws of any other jurisdiction.

                  We have relied as to certain matters on information
obtained from public officials, officers of the Company and other sources
believed by us to be responsible, and we have assumed that the Indenture
relating to the Securities has been duly authorized, executed and delivered
by the Trustee thereunder, an assumption which we have not independently
verified.

                  We hereby consent to the filing of this opinion as an
exhibit to the Registration Statement and to the refer ence to us under the
heading "Validity of the Securities" in



the Prospectus. In giving such consent, we do not thereby admit that we are
in the category of persons whose consent is required under Section 7 of the
Act.

                                   Very truly yours,

                                   SULLIVAN & CROMWELL