BACKGROUND The aim of the study was to investigate whether melatonin has a protective effect against diminished ovarian reserve induced by smoking. METHODS Seventy-two female Wistar-Albino rats were divided into 6 groups: group I (room air), group II (chronic cigarette smoking), group III (room air + 10 mg/kg subcutaneous melatonin), group IV (room air + 20 mg/kg subcutaneous melatonin), group V (chronic cigarette smoking + 10 mg/kg subcutaneous melatonin), group VI (chronic cigarette smoking + 20 mg/kg subcutaneous melatonin). For 45 days, rats were exposed to cigarette smoke through a smoking machine, then subcutaneous melatonin was administered. Apoptotic index, immunohistochemical scoring, ovarian follicle counting, ovarian tissue and serum malondialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) analyses were carried out. RESULTS All of the primordial, primary, secondary and mature follicle numbers were found to be significantly lowered in study groups. Increased HSCORE with anti-caspase-3 staining and a high follicular apoptotic index were demonstrated in the smoking group. Serum and ovarian tissue levels of MDA were found to be elevated with smoke exposure whereas lower MDA levels were determined in melatonin treated groups. Serum and tissue levels of SOD, GPx and CAT were shown to be reduced in the smoking group in comparison with melatonin treated and control groups. 20 mg/kg melatonin administration in the smoking group revealed significantly decreased HSCOREs and apoptotic indices. CONCLUSIONS Cigarette smoking has been definitely shown to be associated with impaired ovarian reserve with respect to significantly diminished numbers of primordial, primary, secondary and mature follicles. Dose-related treatment of melatonin in smokers may provide an evidently reduced apoptotic index and improved antioxidant activity in tissue.