Bone morphogenetic proteins (BMPs) are often used with bone grafts for bone regeneration. The aim of this study was to evaluate the effect of demineralized freeze-dried bone allografts and externally applied rhBMP-2 on bone healing in experimentally generated defects in the calvarium of ovariectomized and nonovariectomized rats via histological and immunohistochemical assays. The current study was carried out on 42 female Wistar rats. After ovariectomy was performed in half of the rats, the rats were divided into three groups: control, allograft, and allograft + BMP. An experimental defect with a diameter of 4 mm was created unilaterally in the parietal bone using a trephine dental drill and a physiodispenser with saline. All animals were euthanized at the end of week 8, and bone tissues were analyzed histologically and immunohistochemically. The allografts produced better results in terms of calvarial defect healing in both the ovariectomized and nonovariectomized groups compared to the control group in enhancing bone healing, whereas BMPs combined with allografts had no positive effect on new bone formation. The allografts and BMPs applied in both groups produced fibrous tissues rather than new bone tissue. Further comprehensive studies on the effectiveness of BMPs in the formation of new bone tissue should be conducted in animals with estrogen deficiency.