Objective: To investigate the impact of electrocoagulation on ovarian reserve after laparoscopic excision of ovarian cysts and the possible mechanisms. Design: A prospective study. Setting: Obstetrics and Gynecology Department of a university hospital. Patient(s): 191 patients with benign ovarian cysts undergoing ovarian cystectomy. Intervention(s): Laparoscopic ovarian cystectomy using bipolar or ultrasonic scalpel electrocoagulation and laparotomic ovarian cystectomy using sutures after the excision of ovarian cysts. Main Outcome Measure(s): Follicle-stimulating hormone (FSH) assay and transvaginal ultrasound evaluating basal antral follicle number, mean ovarian diameter, and ovarian stromal blood flow velocity at day 3 of menstrual cycles 1, 3, 6, and 12 after surgery. Result(s): When comparing the bipolar group and ultrasonic scalpel group with the suture group, a statistically significant increase of the mean FSH value was found in bilateral-cyst patients at 1-, 3-, 6-, and 12-month follow-up evaluations and in unilateral-cyst patients at the 1-month follow-up evaluation. Statistically significant decreases of basal antral follicle number and mean ovarian diameter were found during the 3-, 6-, 12-month follow-up evaluations as well as statistically significant decreases of peak systolic velocity at all of the follow-up evaluations. Conclusion(s): Electrocoagulation after laparoscopic excision of ovarian cysts is associated with a statistically significant reduction in ovarian reserve, which is partly a consequence of the damage to the ovarian vascular system. © 2009 American Society for Reproductive Medicine.