Purpose To determine the first line of infertility treatment for managing patients with unilateral or bilateral ovarian endometriomas. Methods We evaluated pregnancy outcome in patients who had received ovarian surgery for unilateral (Group U, n = 47) or bilateral endometriomas (Group B, n = 38) and aspiration with or without alcohol fixation for unilateral (Group u, n = 37) or bilateral endometriomas (Group b, n = 22). Subsequently, 64 of these women, excluding 29 dropouts, underwent assisted reproductive technology. We compared the clinical pregnancy rates of the four groups. Results The cumulative pregnancy rate after operation of Group B (18%) was significantly lower than that of a cystfree control group (n = 143; 44%) and Group U (43%). Group B had fewer oocytes fertilized during ART than did Group b (P \ 0.005) and fewer blastocysts available for transfer (P \ 0.005). The cumulative pregnancy rate of Group B was also lower than in Group b (P = 0.052). Conclusions Pregnancy outcomes of Group B were not better than for Group b. Therefore, encouraging such women to move directly to ART might help avoid ovarian damage and improve their ability to achieve a pregnancy.