424B3 1 jun2804_424b3.htm 424b3

Filed pursuant to Rule 424(b)(3)
File no. 333-112311

Prospectus Supplement No. 3
(To Prospectus Dated May 20, 2004)

$120,000,000

0.75% Senior Convertible Notes due 2033 and
3,869,172 Shares of Common Stock Issuable Upon Conversion of the Notes

     This prospectus supplement relates to the resale from time to time by the holders of our 0.75% Senior Convertible Notes due 2033 and the shares of common stock issuable upon conversion of the notes.

     You should read this prospectus supplement in conjunction with the prospectus dated May 20, 2004, and this prospectus supplement is qualified by reference to the prospectus, except to the extent that the information in this prospectus supplement supersedes the information contained in the prospectus. The prospectus is to be delivered with this prospectus supplement. The terms of the notes and the common stock issuable upon conversion of the notes are set forth in the prospectus.

     Our common stock is listed on The Nasdaq National Market under the symbol “AFFX.” On June 25, 2004, the reported last sale price of our common stock on The Nasdaq National Market was $31.71 per share.

     Investing in the securities involves risks. See ‘‘Risk Factors’’ on page 6 of the prospectus.

     Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus supplement or the accompanying prospectus is truthful or complete. Any representation to the contrary is a criminal offense.

The date of this prospectus supplement is June 28, 2004.





     The prospectus is hereby amended and supplemented to include in the table under the caption “Selling Securityholders” beginning on page 49 of the prospectus the information regarding the selling securityholders listed below. This information was furnished to us by the selling securityholders as of the date of this prospectus supplement.

  Name   Principal
amount of
notes
beneficially
owned that
may be sold
hereby		   Percentage of
notes
outstanding		   Number of
shares of
common stock
that may be
sold hereby(1)		   Percentage of
common stock
outstanding(2)		   Number of
shares of
common stock
beneficially
owned after
the offering(2)		   Natural person
or persons with
voting or
investment
control		  
 
 
 
 
 
 
 
BNP Paribas Equity Strategies,   $2,391,000   2.0 %   77,093   *   0   Christian  
   SNC                         Menestrier  
                             
CooperNeff Convertible Strategies   $2,573,000   2.1 %   82,961   *   0   Christian  
   (Cayman) Master Fund, LP                         Menestrier  
                             
Deephaven Domestic Convertible   $1,437,000   1.2 %   46,333   *   0   Don McKinnon  
   Trading Ltd.                            
                             
Lyxor/Convertible Arbitrage Fund   $462,000   *     14,896   *   0   Christian  
   Limited                         Menestrier  
                             
Singlehedge US Convertible   $586,000   *     18,894   *   0   Christian  
   Arbitrage Fund                         Menestrier  
                             
Sturgeon Limited   $488,000   *     15,734   *   0   Christian  
                          Menestrier  

* Less than one percent.

(1) Assumes conversion of all of a holder’s notes at a conversion rate of 32.2431 shares per $1,000 principal amount of notes and cash payments in lieu of any fractional interest. This conversion rate, however, is subject to adjustment as described under “Description of Notes—Conversion rate adjustments.” As a result, the number of shares of common stock issuable upon conversion of the notes may increase or decrease in the future.

(2) Calculated based on Rule 13d-3(d)(i) of the Exchange Act using 60,541,858 shares of common stock outstanding as of June 25, 2004. In calculating this amount, we treated as outstanding the number of shares of common stock issuable upon conversion of all of a particular holder’s notes. We did not, however, assume the conversion of any other holder’s notes.

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