Melatonin has anti-oxidant, anti-inflammatory and anti-apoptotic properties. We aimed to investigate the effect of melatonin on the structure and function of mice ovaries following autograft transplantation. NMRI mice were divided into: control, autografted +saline, autografted +melatonin (20 mg/kg/day i.p. injection for 1 day before until 7 days after transplantation). 28 days post transplantation, ovary compartments were studied stereologically. Follicle apoptosis and the level of progesterone and estradiol were also measured. The inflammation, serum MDA concentration and total antioxidant capacity were also assessed on day 7 post transplantation. The total volume of the ovary, cortex and medulla (P < 0.05) and the number of different types of follicles (P < 0.001), the concentration of IL-10, progesterone and estradiol (P < 0.001) and TAC (P < 0.01) significantly decreased in the autografted +saline group compared to the control. The levels of IL-6 (P < 0.01), TNF-α, MDA and the apoptotic rate (P < 0.001) increased significantly in the autografted +saline group compared to the control, while the total volume of the ovary, cortex and medulla (P < 0.05) and the number of different types of follicles (P < 0.001), the concentration of IL-10, progesterone and estradiol (P < 0.001) and TAC (P < 0.01) significantly increased in the autografted +melatonin group compared to the autografted +saline group. The levels of IL-6 (P < 0.01), TNF-α, MDA and the apoptotic rate (P < 0.001) decreased significantly in the autografted +melatonine group compared to the autografted +saline group. In the autografted +melatonin group, the localization of CD31-positive cells in the theca layer was similar to the control group. Melatonin can improve the structure and function of the grafted ovary.