Recently, atelocollagen has been used in tissue engineering as one of the most useful scaffolds for bone formation. However, the optimal scaffold-structure for bone engineering has not been determined. Hence, we compared the honeycomb porous structure (HPS) and the interconnected porous structure (IPS) with or without KUSA/A1 cells in vivo. KUSA/A1 cells alone, HPS alone, IPS alone, KUSA/A1-HPS and KUSA/A1-IPS were implanted in the subcutaneous pockets of 4-weeks-old male SCID mice. The implants were examined radiologically and histologically 1, 2, 4 and 8 weeks after implantation. Radiologically, small radiopaque islands of new bone were observed in the implant of KUSA/A1 cells alone. No radiopacity was observed with both scaffols alone. In the KUSA/A1-HPS implant, the scaffold was partially filled with radiopaque areas. In contrast, in the KUSA/A1-IPS implant, the whole scaffold was filled with a well-defined radiopaque area. Histologically, KUSA/A1 cells alone induced only small nests of new bone. HPS alone produced inflammatory reaction. A large bone was observed in implants of KUSA/A1 cells combined with both scaffolds, but the scaffold was completely filled with new bone without inflammatory reaction within a shorter period in the KUSA/A1-IPS compared to KUSA/A1-HPS implant. Our results indicated that a cotton structured scaffold plays an important role in carrying the cells, providing the precise size, shape and comfortable environment. These results have potential impact to enhance existing therapeutic strategies.