The aim of this study is to evaluate the impact of ovarian endometrioma according to its size on the serum anti-Mullerian hormone (AMH) levels compared to that of other benign ovarian cysts. The current study retrospectively evaluated preoperative serum AMH level and its association to presenting ovarian cyst size which were measured in clinical setting. Women with surgically diagnosed endometrioma or other benign ovarian cysts were included. All patients underwent transvaginal or transrectal ultrasonography to determine the size of the ovarian cysts. Preoperative serum AMH level was checked and evaluated according to histologic type of the cyst, which were endometrioma or other benign ovarian cysts, respectively. Both groups were classified into ≤ 4 cm, > 4 cm and ≤ 8 cm, > 8 cm and ≤ 12 cm, > 12 cm according to the diameter of cyst and analyzed the difference of mean AMH levels in both groups. There was no significant difference in preoperative serum AMH level between the two groups (3.36 ± 2.3 versus 3.76 ± 2.64, p = 0.331). The difference of preoperative AMH levels according to categorized cyst size also was not statistically significant in both groups. Preoperative serum AMH levels were not statistically different between endometrioma and other benign ovarian cyst groups and were not related to the size of endometrioma.