The GeneChip Soybean Genome Array contains approximately 37,500Glycine max (soybean) transcripts, 15,800 transcripts representing the water mold Phytophthora sojae, and over 7,500 transcripts representing Heterodera glycines, a cyst nematode. Soybean is a major source of food worldwide for humans, as well as livestock and dominates the world’s supply of edible vegetable oils. The presence of two important soybean crop pathogens on the Soybean Genome Array enables researchers to gain a better understanding of how the plant interacts with two of its most common pathogens. Sequence information for this array includes public content from GenBank and dbEST. Sequence clusters were created from UniGene Build 13 (November 5, 2003). The Soybean Genome Array was designed in close collaboration with the Soybean Research Community as part of the Affymetrix GeneChip Consortia Program, and provides scientists with a single array which can be used for the study of complex host-pathogen interactions.