Alterations in the length of simple repetitive genomic sequences (microsatellite instability, MSI) may characterize a distinct mechanism of mammary carcinogenesis. In order to investigate whether MSI is associated with chemically-induced mammary carcinogenesis in the rat, 30 microdissected mammary carcinomas were analyzed using 27 different microsatellite markers from chromosomes 1, 3, 5, 7 and 8. DNA was extracted from rat mammary cancer and adjoining microscopically normal tissues from the same slide, amplified by PCR, using different polymorphic DNA markers and the reaction products were analyzed for microsatellite instability. The results of this study indicate that 30% of cases (9 out of 30) showed microsatellite instability at a minimum of 1 locus. Three cases (out of 30) showed microsatellite instability at only three loci or less, called MSI-L (low frequency MSI). Six cases (out of 30) showed MSI at four loci or more, called MSI-H (high frequency MSI). Six cases showed MSI at D5Mit11 and D5Mgh3 loci, five cases showed MSI at D1Mit14, D1Mgh6, D5Mgh5 and D8Mgh10 loci, four cases had MSI at D1Mgh2, and D3Mgh7 loci, three cases had MSI at D3Mit3, D3Mgh5, D7Mgh1 loci, two cases had MSI at D7Mit11 locus and one case had MSI at D3Mgh9 locus. The results of these experiments suggest that MSI may be an important etiological event in the pathophysiology of mammary carcinogenesis.