QuickLinks -- Click here to rapidly navigate through this document

EXHIBIT 21

AFFYMETRIX, INC.
LIST OF SUBSIDIARIES

        Affymetrix, UK Ltd, wholly-owned subsidiary incorporated in the United Kingdom and doing business under such name.

        Affymetrix France S.A.S., wholly-owned subsidiary incorporated in France and doing business under such name.

        Affymetrix GmbH, wholly-owned subsidiary incorporated in Germany and doing business under such name.

        Affymetrix Japan K.K., a wholly-owned subsidiary incorporated in Japan and doing business under such name.

        Affymetrix Pte Ltd, wholly-owned subsidiary incorporated in Singapore and doing business under such name.

        Affymetrix Italia, SRL, wholly-owned subsidiary incorporated in Italy and doing business under such name.

        Anatrace, Inc., wholly-owned subsidiary incorporated in Ohio and doing business under such name.*

        Genetic MicroSystems, Inc., wholly-owned subsidiary incorporated in Massachusetts and doing business under such name.

        Neomorphic, Inc., wholly-owned subsidiary incorporated in California and doing business under such name.

        Pinecone Acquisition, Inc., wholly-owned subsidiary incorporated in California and doing business under such name.

        USB Corporation, wholly-owned subsidiary incorporated in Ohio and doing business under such name.*

        USB Europe, GmbH, wholly-owned subsidiary incorporated in Germany and doing business under such name.*

*

This entity became a wholly-owned subsidiary of Affymetrix, Inc. on January 30, 2008.

QuickLinks

EXHIBIT 21