Bone marrow has been shown to contain a population of rare cells capable of differentiating to the cells that form various tissues. These cells, referred to as mesenchymal stem cells (MSCs), are capable of forming bone when implanted ectopically in an appropriate scaffold. The aim of this study was to investigate the potential of a new β-tricalcium phosphate (β-TCP) as a scaffold and to compare the osteogenic potential between β-TCP and hydroxyapatite (HA). The β-TCP and HA loaded with MSCs were implanted in subcutaneous sites and harvested at 1, 2, 4, and 8 weeks after implantation for biochemical and histological analysis. Biochemically, in both β-TCP and HA composites, the alkaline phosphatase activity in the composites could be detected and was maintained at a high level for 8 weeks. In the histological analysis, active bone formation could be found in both the β-TCP and HA composites. These findings suggest that β-TCP could play a role as a scaffold as well as HA. The fabricated synthetic bone using biodegradable β-TCP as a scaffold in vivo is useful for reconstructing bone, because the scaffold material is absorbed several months after implantation.