Genetic aberrations, such as loss of heterozygosity (LOH) and mutations leading to functional inactivation of the PTEN tumor suppressor gene, located on chromosome 10q23.3, have been shown to be associated with approximately one third of ovarian adenocarcinomas. In addition, microsatellite instability (MSI) leading to the functional inactivation of the PTEN gene has also been reported for ovarian adenocarcinomas with frequencies varying from 6 to 37%. However, the frequency of PTEN gene abnormalities has not been well studied or evaluated in lesions such as typical and atypical endometriosis. The aim of this study was to investigate a possible sequential progression from endometriosis through atypical endometriosis to ovarian carcinoma by assessing LOH at 10q23.3 and MSI in those entities. Genomic DNA was analyzed for LOH and MSI at 3 loci on chromosome 10, using polymerase chain reaction amplification. Significant differences in LOH were seen between endometriosis (4.3%) and ovarian carcinoma (23.5%) at D10S608. The differences at the other 2 loci were not significant. A high frequency of MSI was found in endometriosis (82.6%) and atypical endometriosis (75%); however, the differences were not significant. These results suggest that LOH at D105608 may possibly be an important molecular event in the progression of endometriosis to carcinoma. This study highlights that endometriosis and atypical endometriosis might act as precursor lesions that have the potential to progress into ovarian adenocarcinoma.