Objective: To investigate the relationship between the size of an excised endometrioma and the magnitude of damage to the ovary after the surgery. Design: A retrospective, controlled study. Setting: A university hospital. Patient(s): Eighty-five women with a history of laparoscopic excision of unilateral endometrioma who underwent in vitro fertilization (IVF). Intervention(s): IVF-embryo transfer procedures. Main Outcome Measure(s): Antral follicle counts (AFC), number of dominant follicles (follicles >= 15 mm), and number of oocytes retrieved. Result(s): In the group with cyst diameters of >= 4 cm and group with cyst diameters of < 4 cm, the AFC, number of dominant follicles, and number of oocytes retrieved were decreased in the operated ovaries when compared with those in intact ovaries; in the former group, a statistically significant reduction was observed. The differences of AFC, number of dominant follicles, and number of oocytes retrieved from both ovaries were further compared among the two groups: the decrease in the group with cyst diameters of >= 4 cm was higher than in the group with cyst diameters of < 4 cm. After adjusting for age and AFC in intact ovaries, similar results were obtained, although AFC only showed a tendency. In addition, the receiver operating characteristic curve analysis revealed a statistically significant, positive correlation between the size of excised cysts and the incidence of fewer than four oocytes retrieved from an operated ovary. Conclusion(s): The magnitude of the ovarian damage after laparoscopic endometrioma excision might be related to the size of cyst; the damage to ovaries is more severe when an endometrioma >= 4 cm is excised. ((c) 2013 by American Society for Reproductive Medicine.)