Little is known concerning epithelial metaplastic changes (metaplasia) in ovarian endometriosis. Three hundred fifteen consecutive cases of ovarian endometriosis between 1987 and 1995 were retrieved from hospital files and clinicopathologically analyzed. Two hundred fifty-seven cases were not associated with malignant ovarian epithelial tumor or atypia Four cases were atypical endometriosis. The remaining 54 cases were associated with malignant ovarian epithelial tumor, including borderline tumor. Metaplasias in ovarian endometriosis were observed in 162 (63%) cases not associated with malignant epithelial tumor or atypia. Ciliated cell and eosinophilic metaplasias were the most common (44%, respectively), followed by hobnail (13%) and mucinous (4%) types. Metaplasias in endometriosis were observed in all of the four atypical endometriosis cases and all of the 54 cases with malignant ovarian epithelial tumor. Among these cases, ciliated cell and eosinophilic metaplasia were also the most common. There was no correlation between types of carcinoma and types of metaplasia in endometriosis, but in all of the four Müllerian mucinous borderline tumors, ovarian endometriosis with mucinous metaplasia and hyperplasia was contiguous or intimately associated with the tumor. Metaplasia was often observed in ovarian endometriosis and most frequently was associated with malignant ovarian epithelial tumor or atypia. Metaplastic changes in ovarian endometriosis should not be interpreted as neoplastic features. Mucinous metaplasia and hyperplasia in ovarian endometriosis might be closely associated with the development of Müllerian mucinous borderline tumors.