We have investigated the involvement of microsatellite instability (MSI) and allelic imbalance (AI) at chromosome 13q and 17 in 41 breast and 41 ovarian carcinomas and their association with BRCA1 and BRCA2 gene mutations. MSI was detected in 20% of ovarian and 7% of breast tumors. AI at the BRCA1 locus was detected in 59% and 32% of ovarian and breast tumors, respectively. At the BRCA2 locus, AI rates were 49% and 44% for ovarian and breast tumors, respectively. Germline BRCA1 mutations, identified in 5 (12%) ovarian tumors and in one (2%) breast tumor were not associated with MSI. In only 2/5 BRCA1 positive tumors loss of the wild-type allele was observed. We conclude that BRCA1 mutation status is not associated with MSI and that MSI found in a fraction of ovarian tumors may reflect possible mutations in one of the DNA mismatch repair genes.