DNA fingerprinting using a nonisotopically labeled minisatellite probe provided a valuable technique for genetic monitoring/quality control of laboratory rodents. Each of 12 inbred rat strains had a unique fingerprint pattern, and colonies separated for over 20 years had identical or nearly identical patterns. Strain LOU/Iap, which is known to have been genetically contaminated in the past, was clearly different from strain LOU/CN, supporting previous findings of studies using biochemical markers. Inbred strains of mice were also found to differ from each other. The F1 hybrid between C57BL/6 and CBA/Ca could not be distinguished from C57BL/6 by using DNA fingerprints, although they could be distinguished by using biochemical markers. Some congenic strains differed from their inbred partner. A suspected genetic contamination of MRL/Mp-lpr mice could not be detected in a sample of the breeding colony by using biochemical markers; however, DNA fingerprints from the suspect animals clearly demonstrated genetic segregation. DNA fingerprinting will be of particular value in investigating suspected problems as only a small sample of fresh, frozen, or ethanol-preserved tissue is needed. Thus, the actual suspect animals can be studied, rather than samples from a breeding colony from which contaminated animals may already have been eliminated.