© 2020 Via MedicaBackground: This study presents the evaluation of the damage in the bone tissue resulting from a calvarial defect in rats and the efficiency of exposure to an ozone application with an alloplastic bone graft on the calvarial bone damage. Materials and methods: Wistar male rats (n = 56) were divided into four groups: a control group (n = 14), defect and ozone group (n = 14), defect and graft group (n = 14), and defect, graft, and ozone group (n = 14). Under anaesthesia, a circular full-thickness bone defect was created in all groups, and the experimental groups were further divided into two sub-groups, with 7 rats in each group sacrificed at the end of the 4th and 8th weeks. Bone samples were dissected, fixed in 10% formalin solution, and decalcified with 5% ethylene-diamine-tetraacetic acid (EDTA). After the routine follow-up on tissues, immunostaining of osteopontin and osteonectin antibodies was applied to sections and observed under a light microscope. Results: The control group exhibited osteopontin and osteonectin expression in fibroblasts and inflammatory cells at the end of the 4th week with an acceleration at the 8th week. Ozone administration elucidated new trabecular bone formation by increasing osteoblastic activity. Lastly, our observations underscore that a combination of allograft and ozone application increased the osteoblast, osteocyte, and bone matrix development at the 4th and 8th weeks. Conclusions: Exposure to an ozone application with an alloplastic bone graft on calvarial bone damage may induce osteoblastic activity, matrix development, mature bone cell formation, and new bone formation in rats.