Ovary transplantation is a promising method to preserve fertility in cancerous patients undergoing chemo/ radiotherapy. However, one of the major limitations of this technique is ischemia-reperfusion (IR) injury, which causes serve damage to the follicular cells and decreases the number of follicles in the transplanted ovaries. We aimed to investigate the effect of taurine as an anti-oxidant and anti-apoptotic agent on the histological changes of autotransplanted mouse ovaries. 18 female NMRI mice (4-5 weeks old) were divided into three groups: control, autografted and autografted + taurine (200 mg/kg/day). Mice were treated from 1 day before transplantation until 7 days after. 28 days after transplantation, ovaries were studied stereologically and the percentage of apoptotic follicles was estimated using the TUNEL assay. Data were analyzed using one-way ANOVA and Tukey’s test and the means were considered significantly different at p<0.05. A significant decrease in the total volume of the ovary (p<0.001), volume of the cortex (p<0.001) and medulla (p<0.001) and the number of different types of follicles (p<0.001) was observed in the autografted group compared to the control, whereas the total volume of the ovary (p<0.01), the volume of cortex (p<0.01) and volume of medulla (p<0.04) and the number of different types of follicles (p<0.001) increased significantly in the autografted + taurine group compared to the autografted group. The apoptosis rate increased significantly in the autografted group compared to the control (p<0.001), while it decreased significantly in the autografted + taurine group compared to the autografted group (p<0.001). The results showed that taurine treatment could reduce the IR induced damages to the grafted ovary tissue and improve the follicular survival through reducing apoptosis.