<PAGE>
FILED PURSUANT TO RULE 424(B)(3) PROSPECTUS SUPPLEMENT DATED JUNE 9, 2000
REGISTRATION NO. 333-92577 TO PROSPECTUS DATED FEBRUARY 9, 2000
CUSIP NO. 00826TAB4
AFFYMETRIX, INC.
$150,000,000
5% CONVERTIBLE SUBORDINATED NOTES DUE 2006 AND
1,219,515 SHARES OF COMMON STOCK ISSUABLE UPON CONVERSION OF THE NOTES
This prospectus supplement supplements information contained in the
prospectus dated February 9, 2000 relating to the potential sale from time to
time of up to $150,000,000 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
holder 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>
CIBC World Markets Corp................. 5,092,000 41,398 41,398 --
Deephaven Domestic Convertible Trading
Ltd................................... 2,500,000 20,325 20,325 --
</TABLE>
None of the 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.
