INTRODUCTION: Our aim was to determine the effects of endometrioma by itself and its surgery on ovarian reserve via pre- and postoperative serial measurements of Anti-Mullerian Hormone (AMH) in patients with endometrioma and benign cysts. METHODS: Our study was conducted at an education and research hospital as a prospective controlled clinical trial. Participants were divided according to their diagnosis into endometrioma and non-endometrioma groups. Serial blood samples of the patients for serum AMH levels were collected preoperatively, and postoperatively at the first week, first month, and third month, respectively. Results: A total of 46 patients (25 for the study and 21 for control groups) were included in the study. The mean age of our patients was 31.8±5.57 in the endometrioma group and 29.38±8.64 in the control group. The AMH value was lower in the endometrioma group, but the difference did not reach statistical significance (p>0.05). However, in the postoperative AMH levels measured at the 1st week, 1st month, and 1st year, the values were significantly higher in the non-endometrioma group compared to the endometrioma group (p<0.05). DISCUSSION AND CONCLUSION: According to our study, we can conclude that endometrioma surgery affects ovarian reserve significantly and more negatively than benign cystectomies.