The aim of this study was to investigate the usefulness of AMH levels in the evaluation of surgical impact on ovarian reserve and the differences in postoperative ovarian reserve impairment between endometrioma and non-endometrioma groups. Twenty-four women with benign ovarian masses were enrolled to undergo laparoscopic cystectomy. On day 3 of the cycle preceding the operation and three months after the laparoscopic cystectomy, serum levels of FSH, E2, AMH, and AFC, normal ovarian volumes were measured in all patients in order to determine the influence of the laparoscopic procedure. The mean level of preoperative serum AMH was reduced significantly 3 months after surgery. On the other hand, no significant differences in FSH, E2, AFC, and ovarian volumes were found between the preoperative and 3 months postoperative levels. In a subgroup analysis of the pathologic type of the ovarian cyst, serum AMH levels were significantly decreased postoperatively in the endometrioma group compared with the non-endometrioma group. In conclusion, laparoscopic cystectomy for benign ovarian masses, especially in endometrioma, causes a postoperative decrease in ovarian reserve with associated decreased postoperative AMH levels. Therefore, serum AMH levels may be a valuable biomarker for evaluation of surgical impact on ovarian reserve.