A few studies have investigated the effects of laparoscopic cystectomy for endometrioma on ovarian reserve using serum anti-Müllerian hormone (AMH) levels and have shown inconsistent results. This prospective study was performed to estimate early changes in serum AMH after laparoscopic surgery for endometrioma. In 27 women aged 21-46 years who underwent laparoscopic unilateral cystectomy (n = 13) or oophorectomy (n = 14) for endometrioma, we measured pre- and postoperative serum AMH levels at baseline and 1 week, 1 month, and 3 months after surgery. Serial changes in serum AMH levels were analyzed according to the operation type using analysis of variance. Mean levels of serum AMH decreased significantly immediately after surgery and remained for up to 3 months in both operation types (P = 0.002 for cystectomy group and P <0.001 for oophorectomy group). In addition, the serum AMH levels showed similar patterns of change after cystectomy or oophorectomy. In conclusion, laparoscopic ovarian cystectomy for endometrioma appears to decrease serum AMH levels immediately after surgery.