Affymetrix was founded by Stephen P.A. Fodor , Ph.D. and others in the late 1980s with the revolutionary idea to use semiconductor manufacturing techniques to create GeneChips (an Affymetrix trademark) or generically DNA microarrays. The company has an impressive patent portfolio in this area. Affymetrix was originally a division of Affymax.
The company was spun out of Affymax in 1992. They launched they first product, an HIV genotyping GeneChip, in 1994. Affymetrix went public in 1996.
Acquisitions have included Genetic MicroSystems for slide-based microarrays and scanners and Neomorphic for bioinformatics. In 2000 Perlegen Sciences was spun out to focus on wafer-scale genomics for massive data creation and collection required for characterizing population variance of genomic markers and expression for the drug discovery process.
Early on Affymetrix formed a partnership with Hewlett-Packard Chemical Analysis, now Agilent Life Sciences. That relationship soured and now the two companies are competitors. Today Affymetric manufactures its own scanner hardware.