Background: To establish the clinicopathological and prognostic correlations between endometriosis-associated and non-endometriosis-associated primary ovarian cancer, with a view to providing a reference guide for revision of diagnostic criteria for malignant transformation of endometriosis.Methods: Retrospectively collected clinicopathological and follow-up data of 174 clear cell and endometrial ovarian cancer patients. Cases were divided into endometriosis-associated and non-endometriosis-associated primary ovarian cancer, and comparative analysis of the clinicopathological characteristics and prognosis conducted.Results: Average age and proportion of menopausal patients in the endometriosis-associated ovarian cancer group were lower relative to the primary ovarian cancer group (P<0.05). Other clinicopathological features examined, including body mass index, age at menopause, operation history, dysmenorrhea, complications, tumor size, tumor side, ascites, CA125, HE4, CA199, stage, differentiation, expression of ER, PR, P53, P16, Ki67, MMR, HNF-1β and Napsin A were not significantly different between the groups (P>0.05). Furthermore, rates of resistance to platinum chemotherapy, relapse, progression-free survival and overall survival were comparable between the two groups (P > 0.05).Conclusion: Endometriosis-associated and primary ovarian cancers of the same pathological type are speculated to be homologous in terms of origin from malignant transformation of endometriosis. It may therefore be necessary to revise the diagnostic criteria for ovarian endometriosis malignancy.