BACKGROUND: Ovarian autotransplantation has shown increasing promise as a clinical method for the preservation of fertility and hormonal function. However, information regarding the success rate of this type of transplantation is limited. We hypothesized that results vary according to the site of the ovarian transplantation. To test this hypothesis, fresh or cryopreserved ovarian strips were autotransplanted to orthotopic or heterotopic sites. The strips were later collected, and the morphology and expression of selected markers of apoptosis were evaluated. We compared the Bax, Bcl-2 and cleaved caspase-3 staining levels and the morphometric aspects of autotransplanted fresh and cryopreserved ovarian strips placed at orthotopic and heterotopic sites in minipigs. METHODS: Forty female minipigs were allocated to the following five groups: group 1 (control), ovarian tissue removed during oophorectomy; group 2, transplantation of fresh ovarian strips to a heterotopic site; group 3, transplantation of fresh ovarian strips to an orthotopic site; group 4, transplantation of cryopreserved ovarian strips to a heterotopic site; and group 5, transplantation of ovarian trips to an orthotopic site. On day 7 after transplantation, ovarian strips were collected, and the morphology and expression of apoptosis markers were evaluated. RESULTS: In all groups, follicles across all stages of development were detected. The numbers of primordial, primary and secondary follicles were similar in all groups, but the numbers of antral follicles were lower in the cryopreserved groups in comparison with freshly derived ovarian tissue, with no significant differences observed between fresh and cryopreserved transplants. In all transplanted groups, Bcl-2 expression was lower and Bax expression was higher than in the control group. Furthermore, increased expression of apoptosis markers was detected in fresh intraperitoneal transplants. Lastly, the expression of cleaved caspase-3 was higher in the cryopreserved orthotopic group compared with the heterotopic group. CONCLUSIONS: Orthotopic and heterotopic ovarian strip transplantations are feasible options using these techniques. Importantly, we found that heterotopic transplantation preserves ovarian follicle integrity to a greater degree (i.e., lower expression of apoptosis markers) than orthotopic transplantation, and cryopreservation does not exacerbate expression of apoptosis's markers. These findings have major clinical applications and enhance the discussion regarding the heterotopic transplantation of ovarian tissue.