Periodontitis is a common chronic infection of dental tissues. Ozone therapy (OT) and low level laser therapy (LLLT) are useful treatments for periodontitis. We investigated the effects of OT and LLLT on periodontal disease-induced bone destruction in rats with experimentally induced periodontitis (EP). We used 30 male Wistar rats divided into three groups: control, OT and LLLT. EP was induced by placing a 3.0 silk suture around the cervix of the left mandibular first molar tooth. OT was performed using an ozone generator at 80% concentration. LLLT was applied using a diode laser. Both OT and LLLT were performed for two weeks at two day intervals. Histomorphometric and immunohistochemical analyses also were performed. Alveolar bone loss was significantly less in the LLLT group compared to the control group. The number of HIF-1 alpha positive cells was significantly less in the LLLT group compared to the control group. We found significantly fewer RANKL-positive cells in the OT group compared to the control group. The number of osteoprotegerin (OPG) positive cells was significantly greater for the LLLT group than for the control group. Although both treatments produced positive effects, LLLT appears to be more effective for increasing alveolar bone formation.