Biological apatite presented in bone and teeth of mammals contains various minerals; thus, it has lots of defects with nano-scale sizes in the crystal structure. We fabricated hydroxyapatite ceramics including bone minerals (bone HAp ceramics) as model materials to clarify the relationship between nano-defect structure and bioactivity of biological apatite. The X-ray diffraction (XRD) results indicated that crystalline phase of pure and bone HAp ceramics were of HAp single phase. Chemical compositions of pure and bone HAp did not change before and after firing at 1000 °C for 5 h. Microstructure observed by high-resolution transmission electron microscope (HR-TEM) indicated that bone HAp ceramics contained more defects and strains compared to pure HAp ceramics. Osteoblasts derived from rat bone marrow cells (RBMC) were seeded on both pure and bone HAp ceramics. The level of differentiation into osteoblasts was examined by determining the content of alkaline phosphatase (ALP) for initial/middle stage and osteocalcin (OC) for late stage. The ALP activity normalized for DNA content of osteoblasts cultured on the bone HAp ceramics was higher than that of pure HAp ceramics. The OC amount normalized for DNA content of bone HAp ceramics was the almost same as that of pure HAp ceramics. These results demonstrate that the bone HAp ceramics may promote the differentiation into osteoblast.