Background: MSCs may improve ovary transplantation through the secretion of angiogenic and anti apoptotic factors. The aim of this study was to investigate the effect of rat Bone Marrow Mesenchymal Stem Cells (rBMSCs) transplantation on the mice ovary structure and function following auto transplantation. Methods: NMRI mice (4-5 weeks old) were divided into three groups (n=6): control (freshly isolated ovaries), transplanted + rBMSCs (1×106 cells per 5µl saline solution) and transplanted (5µl saline solution). rBMSCs and saline solution were injected into the grafted ovaries at the time of transplantation. 7 days after ovarian transplantation, the starting day of estrous cycle was determined. 28 days after ovarian transplantation, the ovaries were stereologically studied and the plasma levels of estradiol and progesterone hormones were evaluated. The results were analyzed using one-way ANOVA and Tukeys test and the means were considered significantly different at P. Result: A significant reduction in the mean total volume of ovary, cortex and medulla, the number of follicles, the levels of estradiol and progesterone and the estrous cycle recovery rate was found in the transplanted group when compared to the control. However, the mentioned parameters increased significantly in the transplanted + BMSCs group compared to the transplanted group. Conclusion: The injection of BMSCs into the grafted ovaries improve their structure and function and could be considered as a new method in the field of ovary transplantation to achieve better results.