Background: Endometriosis is a common gynecological disease and exact pathogenesis is still unclear. Recently, an increasing interest has been given to the potential role of stem cells in the development of endometriosis. The aim of this study was to test the expression of stemness-related markers CD133 and ABCG2 in endometriosis. Materials and Methods: CD133 and ABCG2 protein expression in eutopic and ectopic endometrial tissue with endometriosis and endometrium tissue without endometriosis were examined by Western blot. Results: Eutopic endometrium showed high level of CD133 and ABCG2 protein when compared with ectopic endometrium (p = 0.042, p = 0.038) and control endometrium (p = 0.000, p = 0.000). The expression of CD133 protein in ectopic endometrium was positively correlated with R-AFS score of endometriosis (p = 0.000, r = 0.793) and no significant relation was noted between ABCG2 and R-AFS score (p = 0.563). Two of three patients with recurrence had much higher expression of ABCG2 protein than the patients without recurrence. Conclusion: Aberrant expression of CD133 and ABCG2 in eutopic and ectopic endometrial tissue with endometriosis suggests that they are probably associated with the pathogenesis of endometriosis and stem cells play a possible role in its development.