Carbonate apatite (CO3Ap) is an inorganic component of bone. This study aimed to compare the composition and tissue response to of CO3Ap (CO3Ap-DP) fabricated by the dissolution-precipitation reaction using calcite as a precursor and Bio-Oss®, which is widely used in orthopedic and dental fields as a synthetic bone substitute. X-ray diffraction and Fourier transform infrared results showed that CO3Ap-DP and Bio-Oss® were both B-type carbonate apatite with low crystallinity. The average sizes of CO3Ap-DP and Bio-Oss® granules were 450 ± 58 and 667 ± 168μ m, respectively, and their carbonate contents were 12.1 ± 0.6 and 5.6 ± 0.1 wt%, respectively. CO3Ap-DP had a larger amount of CO3 than Bio-Oss® but higher crystallinity than Bio-Oss®. When a bone defect made at the femur of rabbits was reconstructed with CO3Ap-DP and Bio-Oss®, CO3Ap-DP granules were partially replaced with bone, whereas Bio-Oss® remained at 8 weeks after implantation. CO3Ap-DP granules elicited a significantly larger amount of new bone formation at the cortical bone portion than Bio-Oss® at 4 weeks after the implantation. The results obtained in the present study demonstrated that CO3Ap-DP and Bio-Oss® showed different behavior even though they were both classified as CO3Ap. The CO3 content in CO3Ap played a more important role than the crystallinity of CO3Ap for replacement to bone and high osteoconductivity.