Objectives The aim of this study is to investigate the effect of the graft material combined with ozonized blood on bone healing in rabbit in maxillary sinus lifting applications histomorphometrically, immunohistochemically and microtomographically. Materials and Methods Twenty-eight New Zealand rabbits were randomly divided into 2 groups as experimental (n = 14) and control (n = 14). In experimental group, 5 ml (milliliter) blood obtained from the ear vein of each rabbit was ozonized by 80 mu l (mu l)/ml concentration ozone-oxygen mixture. Graft material was combined with this ozonized blood. In control group, the graft was combined with saline solution at 0.9% concentration. A 5 mm (millimeter) in diameter window was created on right maxillary sinus window in each rabbit under general anesthesia by local anesthesia support. Sinus membrane was elevated and the space was augmented by 1 cc (cubic centimeter) graft material. One rabbit from the control group which was planned to sacrifice at the end of 8 weeks could not participate in the evaluation because of the extensive inflammation at the operation site. Newly formed bone area and bone density were measured using by image analysis program. Bone morphogenetic protein-2 (BMP-2), vascular endothelial growth factor (VEGF) and collagen-1 (COL-1) analyses were carried out immunohistochemically. The amount of the newly generated bone and the amount of the total augmented space were calculated volumetrically by microtomography. Results According to histomorphometrical analysis, although newly formed bone area has increased in both experimental and control group with time, statistically significant results were obtained when only O-8 (ozone-treated experimental group planned to be sacrificed after 8 weeks) and O-4 (ozone-treated experimental group planned to be sacrificed after 4 weeks) groups were compared (p = 0,037). The increase in new bone density was seen in both experimental and control groups with time and the results were statistically significant when O-8 group compared to O-4 and C-4 group (ozone-free control group planned to be sacrificed after 4 weeks) (p = 0,07 and p = 0,04, respectively) and C-8 (ozone-free control group planned to be sacrificed after 8 weeks) group compared to C-4 group (p = 0,023). According to immunohistochemical analysis, the intensity and the severity of field staining with anti-BMP-2 have increased in experimental group whereas it has decreased in control group but despite that there was no statistically significance among all groups compared to each other. The number of new vessels stained with anti-VEGF has increased in both experimental and control group with time and multiple comparison results were statistically significant when O-8 group compared with O-4 and C-4 (p = 0,000, p = 0,000, respectively), O-4 group compared with C-8 (p = 0,000) and C-8 group compared with C-4 (p = 0,000). Although the intensity and the severity of field staining with anti-COL-1 have increased in both experimental and control group with time, there was no statistically significance among all groups compared to each other. According to microtomographical analysis, the percentage of the volume of the newly generated bone in the total augmented space volume has decreased with time in both experimental and control groups. Conclusions Considering the results of this study, the graft material combined with the ozonized blood increased the density of the newly generated bone and the number of new vessels in maxillary sinus lifting applications in rabbits.