Calcium phosphate bioceramics has recently experienced increased interest in bone reconstruction. Mimicking of natural structure of bone, like the use of nanomaterials, is an attractive approach for generating scaffolds for bone regeneration. The aim of present study was to evaluate the effect of nanonization on the biphasic calcium phosphate (BCP) ceramic in the repair of bone cavities in the canine mandible. A commercial BCP was dry-milled in a high energy planetary ball mill with zirconia balls and container. Three holes (8 mm in diameter) were outlined to the depth of cortical bone of mandibular angle of 5 dogs bilaterally. The first hole (positive control group A, n = 10) was filled in with commercial BCP material. The second hole was loaded with the nanonized BCP (experimental group C, n = 10) and the third one was left untreated (negative control group B, n = 10). The defects were allowed to regenerate for 8 weeks. New bone formation was greater in groups A and C than in B. No difference was seen between group A and group C (P = 0.676). The residual bone material in group C (19.34 ± 8.03) was as much as one-half of that in group A (38.69 ± 7.90%) (P = 0.000). The negative control group B presented the highest amount of soft tissue within the bone defects. The least percentage of marrow space was found in the positive control group (13.23 ± 13.52). Our results depicted that the rate of resorption increased significantly after nanonization even though the nano-sized BCP failed to make a superior regeneration than the ordinary BCP.