Recent molecular and pathological evidence suggests that endometriosis is a monoclonal, neoplastic disease. Moreover, endometriosis serves as a precursor of ovarian cancer (endometriosis-associated ovarian cancer; EAOC), especially of the endometrioid and clear cell subtypes. Although a variety of molecular events, such as p53 alteration, PTEN silencing, K-ras mutations, and HNF-1 activation, have been identified in EAOC, its precise carcinogenic mechanism remains poorly understood. Our recent data indicate that microenvironmental factors, including oxidative stress and inflammation, play an important role in the carcinogenesis and phenotype of EAOC. The management of endometriosis from the standpoint of EAOC is not standardized yet. To this end, clarification of the precise natural course and the risk factors that contribute to malignant transformation remain important goals. Among the phenotypes of EAOC, clear cell carcinoma, seems to require a specific treatment strategy, including molecular targeting.