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Radiation therapy may compromise the quality of bone around dental implants, and its ability to regenerate, remodel, and revascularize. This study aimed to describe the irradiation effect on the bone microstructure of the mandible using dental implants in a canine model. Five beagle dogs were exposed to 40 Gy fractionated radiation. In total, 20 dental implants were inserted, two in the irradiated and two in the non-irradiated side. The mandible bone blocks were subjected to 3D micro-computed tomography (µCT) imaging, later evaluated histomorphometrically by light microscopy and scanning electron microscopy. Alterations in irradiated bone were observed under µCT imaging showing an increased anisotropy, porosity, and pore volume. Bone surface-to-bone volume decreased. The bone to implant contact index was significantly reduced in the irradiated bone (75.6% ± 5.8%) as compared to the non-irradiated bone (85.1% ± 6.8%). In the irradiated mandible, osteocytes with their filopodial processes, the bone beneath the periosteum, and subperiosteal veins showed structural differences but were not significant, whereas the diameter of Haversian canals were smaller statistical significant as compared to the control side. The study highlights that radiation dosage of fractioned 40 Gy causes alterations in the alveolar bone microstructure with compatible osseointegration and clinically stable dental implants.