Human bone marrow mesenchymal stem cells (hMSCs), one of the tissue stem cells, have the ability to differentiate into adipocytes, osteoblasts or chondrocytes, leading to the attempt to apply these stem cells to regeneration of bone and cartilage. To analyze characteristics of these cells and explain pluripotency of hMSCs, we analyzed gene expression profiles of hMSC clones by using DNA chips that contain over 10,000 genes per chip. We also analyzed their proliferation rates and cell surface markers. As a result, these hMSC clones showed various proliferation rates indicating that hMSCs contains multiple types of cells in their population. Furthermore, analysis of surface markers, especially analysis of CD34 and CD44 showed that these stem cells are not hematopoietic stem cells but mesenchymal origin. Profiling of gene expression by using DNA chip showed that several genes were specifically expressed in hMSCs, and the highest expression was observed in clone no. 12 showing that this clone possesses unique characters as a MSC applicable to regeneration research and regenerative medicine.