<PAGE>
PROSPECTUS SUPPLEMENT DATED JULY 19, 2000 FILED PURSUANT TO RULE 424(b)(3)
TO PROSPECTUS DATED JULY 11, 2000 REGISTRATION NO. 333-36790
CUSIP NO. 00826TAD0
AFFYMETRIX, INC.
$225,000,000
4 3/4% CONVERTIBLE SUBORDINATED NOTES DUE 2007 AND
700,943 SHARES OF COMMON STOCK ISSUABLE UPON CONVERSION OF THE NOTES
This prospectus supplement supplements information contained in the
prospectus dated July 11, 2000 relating to the potential sale from time to time
of up to $225,000,000 aggregate amount of notes and the common stock into which
the notes are convertible. This prospectus supplement is not complete without,
and may not be delivered or utilized except in connection with, the prospectus,
including any amendments or supplements to it.
The following table supplements the information set forth in the prospectus
under the caption "Selling Security Holders" with respect to the selling holders
and the respective principal amounts of notes beneficially owned by the selling
holders that may be offered pursuant to the prospectus, as amended or
supplemented:
<TABLE>
<CAPTION>
PRINCIPAL AMOUNT COMMON STOCK COMMON STOCK
OF NOTES ISSUABLE UPON OWNED AFTER
BENEFICIALLY OWNED CONVERSION OF COMMON STOCK COMPLETION OF
NAME AND OFFERED THE NOTES OFFERED THE OFFERING
---- ------------------ ------------- ------------- -------------
<S> <C> <C> <C> <C>
Robertson Stephens...................... $4,000,000 12,461 12,461 --
</TABLE>
The line items "Credit Suisse First Boston Corporation... $3,000,000, 9,346,
9,346, --" and "Partners Reinsurance Company, Ltd.... $365,000, 1,137,
1,137, --" contained in the table set forth in the prospectus under the caption
"Selling Security Holders" shall be deleted in their entirety and replaced with
the following:
<TABLE>
<CAPTION>
<S> <C> <C> <C> <C>
Credit Suisse First Boston
Corporation........................... $29,183,000 90,913 90,913 --
Partners Reinsurance Company............ $ 425,000 1,324 1,324 --
</TABLE>
None of the above selling holders nor any of their affiliates, officers,
directors or principal equity holders has held any position or office or has had
any material relationship with us within the past three years, except that
Credit Suisse First Boston and Robertson Stephens were initial purchasers in
connection with the offer and sale of the notes in February 2000 and from time
to time perform investment banking services, for which they receive customary
fees.
