Using agarose gel electrophoresis, we surveyed four strains of inbred mice (AKR/J, C57BL/J, LG/J, and SM/J) for 472 microsatellite loci. Agarose electrophoresis proved to be extremely efficient in separating alleles differing by six or more base pairs and detected a majority of allelic differences of between two and six base pairs. Overall, 64.4% of loci showed polymorphism among the four strains, and pairwise comparisons ranged from 42.1% to 48.1%. Microsatellite polymorphism for strains LG/J and SM/J has not been previously described and was sufficiently high (47.1%) to make these size-divergent strains excellent candidates for quantitative trait loci (QTL) analysis of normal growth.