There are some side effects of isotretinoin in many organs. However, a study investigating the effects of isotretinoin on the human ovarian reserve has not been reported previously. The study was conducted to investigate possible effects of isotretinoin on ovarian reserve. Serum anti-Müllerian hormone (AMH) levels were measured at the beginning and at the end of isotretinoin treatment in 22 patients with acne and in 22 women without. The mean AMH level before treatment was 5.77 ng/mL in the study group and 3.79 ng/mL in the control group (p = 0.008). Following treatment, the mean AMH level was 4.69 ng/mL in the study group. This mean AMH level after treatment was statistically lower than the AMH level before treatment (p = 0.012). There was no significant difference between the mean AMH level at the end of treatment and that of the control group (p = 0.20). The high level of pre-treatment AMH levels could be an evidence of hyperandrogenism in women with acne, even if they are not identified as having polycystic ovary syndrome (PCOS) or hyperandrogenism. Decrease in AMH levels following exposure to isotretinoin may suggest that it has a detrimental effect on the ovaries.