Genetic profiles for 46 microsatellite loci of 12 inbred strains of rats, including 2 congenic strains and a coisogenic strain, have been demonstrated. Rates of loci with different alleles between 2 inbred strains, which are not closely related to each other in origin, were from 71.7% between ACI/N and IS/Kyo strains to 41.3% between F344/N and TM/Kyo. On the other hand, the rates were 0% in both of 2 sets of congenic strains; between F344/N and F344/N-rnu, or between BN/fMaiKyo and BN.IS. When WTC/Kyo and the coisogenic strain TRM/Kyo (WTC/Kyo-tm) were compared for 115 microsatellite loci, no loci with different alleles between the strains were found. The 46 loci should be useful as genetic monitoring markers, since all of the primer pairs generate distinct PCR-products at a fixed annealing temperature of 55 degrees C.