The purpose of the study reported here was to identify, by size, a set of microsatellite markers for use in diagnostic genetic monitoring of FVB/N mouse colonies. A large panel of microsatellite markers were chosen on the basis oftheir high degree of allelic variability. These markers were then tested for their ability to amplify well under a standard set of polymerase chain reaction analysis conditions and to present an easily identifiable band on an agarose gel. From this panel, we chose at least one marker on each chromosome that amplified well under our standard high-throughput conditions. Using this approach, we identified the allele sizes for 27 microsatellite markers in the FVB/N strain of mice. Each autosomal chromosome and the X chromosome were analyzed using at least one locus marker. We have determined a precise size for FVB/N microsatellite alleles, as opposed to a description of size in relation to that of a known allele.