A porous hydroxyapatite/collagen composite (HAp/Col) was developed that consists of hydroxyapatite nanocrystals and atelocollagen. In this study, cylindrical (diameter: 5 mm, height: 3 mm) porous HAp/Col implants with different pore sizes (diameter: 160 or 290 microm) were prepared, and the influences of pore size and implanted volume were evaluated using a rabbit bone defect model. In the implant groups, one or three (diameter: 5 mm, total height: 9 mm) implants were transplanted into bone holes created in the anteromedial site of the proximal tibiae, while a group without implantation was used as a control. Histological observation revealed that at two weeks after implantation, bone formation was initiated not only from the periosteum but in regions where the implants bordered on bone marrow. At four weeks, bone formation expanded from the marrow cavity side into the center of the implants, particularly in those implants with large pores. At twelve weeks, four implant groups showed repair of cortical defects and implant absorption, which was thought to be the result of natural bone remodeling mechanisms. The control group showed bone formation developed from the periosteum without bone induction in the marrow cavity, and at four weeks, the bone hole was almost healed. pQCT analysis revealed that the expansion rates of bone tissue were higher in the large-pore implant groups than in the small-pore groups. These data demonstrate the osteoconductivity of porous HAp/Col and the importance of its porous structure.