Hydroxyapatite and carbonate apatites with different carbonate contents were synthesized, mixed with atelocollagen, and made into sponge scaffolds. The scaffolds were implanted into the bone sockets of the femurs of male New Zealand white rabbits for 2, 3, 12 and 24 weeks. carbonate apatite-collagen scaffold with 4.8 wt% carbonate content appeared to have similar crystallinity and chemical composition to human bone. When the scaffolds were implanted into the rabbit femurs, histological observation indicated that the carbonate apatites-collagen scaffolds with relatively higher carbonate contents were gradually deformed throughout the implantation period, and showed uniform surrounding bone after 24 weeks and could not be distinguished. The carbonate apatite-collagen scaffold with 4.8 wt% carbonate content showed the highest bone area ratio of all of the scaffolds. It is suggested that a carbonate apatite-collagen scaffold with carbonate content similar to that of human bone may have optimal bone formation ability.