Hydroxyapatite (HAp) and biphasic calcium phosphate (BCP) nano powders were synthesized using the microwave-assisted synthesis process dependent on pH and microwave irradiation time. The average size of a powder was less than 100 nm in diameter. Through in-vitro cytotoxicity tests by an extract dilution method, the HAp and BCP nano powders have shown to be cytocompatible for L-929 fibroblast cells, osteoblastlike MG-63 cells and osteoclast-like Raw 264.7 cells. The activation of osteoblast was estimated by alkaline phosphatase (ALP) activity. When the HAp and BCP were treated to MG-63 cells, alkaline phosphatase activities increased on day 3, compared with those of the untreated cells. Also, the collagen fibers increased when the HAp and BCP powders suspension were treated to MG-63 cells, compared to those of the untreated cells. Quantitative alizarin red S mineralization assays showed a trend toward increasing mineralization in osteoblast cultured with powder suspension. In conclusion, hydroxyapatite and biphasic calcium phosphate appeared to be a bone graft substitute material with optimal biocompatibility and could be further applied to clinical use as an artificial bone graft substitute.