The average survival was found to be different between substrains of rats, F344/Du and F344/N. One of the causes of this difference could have been genetic contamination by crossbreeding with other strain(s) after the divergence of substrains. These two strains were examined by PCR-SSLP (simple sequence length polymorphism) procedure using microsatellite (Mit) markers to identify the contamination. All 288 Mit markers distributed throughout the genome exhibited no size polymorphisms between these two strains. This indicated that there was no genetic contamination between these two strains. The phenotypic difference in average survival, thus, is not due to genetic contamination.