This paper describes the use of the program e-pcr to localize 687 known major histocompatability complex (MHC) microsatellite primer pairs to their sequence positions in several genomic assemblies across the MHC region. The sequences used were the Sequences of Sanger Institute's MHC Haplotype Project COX, PGF, QBL, as well as the Celera, and Reference (PGF across extended MHC) sequences from the NCBI genomic build 36. More than 95% (664/687) of the markers mapped unambiguously to the Reference assembly sequence. All primer pairs used in this analysis, and those were previously unknown to UniSTS, have now been assigned permanent public UniSTS identifiers. Mapping and descriptive data for each primer pair are available at the publicly accessible dbMHC microsatellite resource http//www.ncbi.nlm.nih.gov/projects/mhc/xslcgi.fcgi?cmd=mssearch.