© 2017 American Association of Oral and Maxillofacial Surgeons Purpose: The aim of the present study was to evaluate the effect of alendronate (ALN) on the bone microarchitecture of irradiated rats with estrogen deficiency, using microcomputed tomography (micro-CT) and histomorphometric analysis. Materials and Methods: Forty adult Wistar rats were subjected to ovariectomy and randomly divided into the following groups: control (CON), ALN, irradiated (IRR), and ALN/irradiated (ALN/IRR). Approximately 50 days after ovariectomy, the hind limbs of the rats in the IRR and ALN/IRR groups were irradiated with 15 Gy of x-radiation. The rats were euthanized 7 and 30 days after irradiation. The bone microarchitecture was analyzed using micro-CT and histomorphometry. The bone microarchitecture was evaluated using the Mann-Whitney U test, analysis of variance, and the post hoc Tukey test, with statistical significance set at 5%. Results: Irradiation had increased the thickness of the cortical bone at 7 days (P <.05) and also decreased the number of trabeculae per unit length and increased the average distance between the trabeculae (P <.05) at 30 days. ALN inhibited the deleterious effect of x-radiation, preventing the distance between the trabeculae from increasing and the number of trabeculae per unit length from decreasing (P <.05). Conclusions: The present results have demonstrated that the initial effect of ALN could be positive, because it checked the deleterious action in the bone tissue submitted to x-radiation.