Purpose To assess outcomes in assisted reproductive technology (ART) in infertile women with endometriosis with respect to their concomitant endometrioma status and surgical history in our department. Methods This is a retrospective case control study which analyzes informational data obtained at a university hospital. The study drew from a patient pool of 332 cases (877 cIVF/ICSI cycles) that took place in our department from 2006 to 2008. Sixty-one cases (97 cycles) had major indications for cIVF/ICSI with endometriosis. We classified groups from these 61 cases as follows: an unoperated endometrioma group (A) with 31 cycles, a postoperative endometrioma group (B) with 51 cycles, and a no endometrioma group (C) with 15 cycles. We analyzed and compared these three groups and also included a nonendometriosis tubal infertility group (D) with 27 cycles. Results In the control group (D), serum FSH levels and the cancellation rates were significantly lower than those of other groups, and the number of developing follicles was higher. E2 levels before oocyte aspiration in the postoperative endometrioma group (B) was lower. Implantation, pregnancy, delivery and miscarriage rates were not significantly different among the four groups. Conclusion The results suggest that endometriosis causes a decrease in endocrinologic ovarian function whether or not an endometrioma is also present. As for E2 level before oocyte aspiration, our results suggest that ovarian reserves might be reduced by endometrioma excision, but this is difficult to evaluate. In the endometriosis groups, cancellation rates were significantly higher, although when embryos were transferred the pregnancy rates were not significantly different when compared with the non-endometriosis group. As for infertile women with endometriomas, our results suggest that preexisting ovarian reserve is reduced by the presence of endometriosis, and ovarian reserve might also be reduced by excision of endometriomas.