Purpose: The purpose of this study was to evaluate bone repair with two bone substitutes, deproteinized bovine bone and biphasic calcium phosphate ceramics, associated with autogenous bone. Materials and Methods: The experimental groups were as follows: autogenous bone only (AB), autogenous bone/deproteinized bovine bone (1:1), and autogenous bone/biphasic calcium phosphate ceramic (1:1). After 30, 60, and 90 days, animals were euthanized and samples were collected for microcomputed tomography (micro-CT), histologic, histomorphometric, and expression analyses of VEGFA, RUNX2, ALP, COL1A1, OCN, PHEX, RANKL, and OPG genes by real-time polymerase chain reaction (PCR) array. Results: Histomorphometric analysis showed no difference in the amount of immature bone between AB and AB/biphasic calcium phosphate ceramic at 30 and 60 days. There was less mature bone formation in the AB/deproteinized bovine bone at 60 days compared with AB/biphasic calcium phosphate ceramic and AB, and a lower amount of immature bone in the AB/deproteinized bovine bone at 30 and 60 days compared with the AB (P ≤ .05). Micro-CT analysis showed higher immature bone volume (BVI) in the AB/biphasic calcium phosphate ceramic at 60 days and lower BVI at 90 days (P ≤ .05). Molecular analysis showed a lower expression of all genes in the AB/deproteinized bovine bone and AB/biphasic calcium phosphate ceramic compared with AB at all time points. A greater expression of RANKL was found in the AB/deproteinized bovine bone compared with AB/biphasic calcium phosphate ceramic at 30 days (P ≤ .05), and a lower expression of the OC, RUNX2, and ALP genes in AB/deproteinized bovine bone and AB/biphasic calcium phosphate ceramic was found compared with AB at all time points (P ≤ .05). Conclusion: The use of biphasic calcium phosphate ceramic resulted in greater immature bone formation than deproteinized bovine bone at an early assessment. The studied bone regeneration genes were downregulated in comparison to the control. Keywords: autogenous bone, biomaterials, bone formation, bone substitutes, deproteinized bovine bone, hydroxyapatite