Background/aim: This study explores the effects of ozone and propolis on the healing of critically sized bone defects at both the histologic and molecular levels, and the locations and concentrations of osteopontin and osteonectin during healing; both proteins play roles during bone healing. Materials and methods: This study used 56 adult male Sprague-Dawley rats of an average weight of 350 g, divided into four groups of 14: a control group, a topical ozone group (O), a topical ozone + systemic propolis (O + PO) group, and a systemic propolis group (PO). Seven rats from each group were sacrificed at the end of week 4 and the other seven at the end of week 6. Tissues were subjected to histologic and immunohistochemical examinations in a fixative solution. The results were analyzed using the statistical software package SPSS 23 (Statistical Package for the Social Sciences—IBM). Results were considered significant at the 95% confidence level (P<0.05). Results: Graft sections were immunostained for osteonectin. Staining was low in the control group but moderate in the other three groups; the differences were significant. The three experimental groups did not differ significantly. Graft sections were also immunostained for osteonectin. At 4 weeks, staining was low in the control group but moderate in the other 3 groups. At 6 weeks, stronger staining was apparent in the 3 experimental groups. At both 4 and 6 weeks, the differences between the control and experimental groups were significantly different, but the differences among the experimental groups were not. Conclusion: The authors' results are compatible with the literature. Ozone and propolis, given separately or together, improved bone healing, increased bone formation, and reduced bone destruction. However, further research is required.