To determine the chromosomal locations for genes expressed in porcine Peyer's patches, polymerase chain reaction-based mapping of expressed sequence tags (ESTs) isolated from a porcine Peyer's patch-specific cDNA library was performed across a 6500-rad swine radiation hybrid panel. A total of 116 ESTs were mapped with LOD scores >6.0, and another 11 ESTs had LOD scores between 5.0 and 6.0. Of these 127 ESTs, 63% matched known genes (<e-25), 26% matched genes of unknown function, and 11% matched no sequences in the public mammalian databases. Comparative mapping information for 91% of the unknown ESTs was obtained in silico by sequence matching to human chromosomes. Placement of these ESTs on the porcine map will assist in the development of high density and comparative genetic maps for positional cloning and identification of genes responsible for immune function in the gut.