The aim was to investigate the effect of injecting adipose derived mesenchymal stem cells (ADSCs) on reducing oxidative stress, inflammation and improving the structure and function of the autografted ovaries through stereological and biochemical evaluations. Mice (4–5 weeks old) were divided into three groups: control, autograft, and autograft +ADSCs (six mice per group). 7 days after ovary autografting and ADSCs injection, serum concentrations of IL-6, TNF-α and IL-10, malondialdehyde and superoxide dismutase activity were measured. On day 28, ovary histology and CD31 expression was assessed. Serum concentrations of progesterone and estradiol were also estimated. in the autograft +ADSCs group, the total volume of the ovary and the volume of the cortex, the number of follicles, the serum concentrations of IL10, estradiol and SOD activity significantly increased compared to the autograft group(P ≤0.05). Serum concentrations of IL6, TNFα and MDA in the autograft +ADSCs group were significantly lower than the autograft group (P ≤0.05). The localization of CD31-positive cells in the theca layer of follicles improved to the control level following ADSCs transplantation. The ability of ADSCs to reduce oxidative stress and inflammation probably plays a considerable role in improving the structure and function of the autografted ovaries.