Because microsatellite markers have a high degree of genetic variability, they are an effective tool for genetic monitoring. We have developed a genotyping panel containing 87 microsatellite markers that are polymorphic among commonly used inbred rat strains, including ACI, Fischer 344, Lewis, Brown Norway, Wistar-Furth, and Wistar-Kyoto. The markers are located at approximately 15- to 20-cM intervals along each of the 20 autosomes. By using fluorescently labeled primers and multiplex PCR analysis, the entire genome can be assayed with only 8 reactions. The resulting amplicons from these reactions can be distinguished from one another by both their size and the fluorescent dye associated with them. Amplicons are analyzed and allele sizes are determined by using automated capillary-based instrumentation. These multiplex panels provide a cost-effective and rapid method for genetic monitoring for applications ranging from assessing genetic contamination in a rat colony to moving mutations from one genetic background to another by using a speed congenic approach.