Effects of mesenchymal stem cells (MSCs) on graft-versus-host disease (GVHD) have been actively investigated since the discovery of the immunomodulation property of MSCs about a decade ago. Human clonal MSCs (hcMSCs) were isolated from human bone marrow aspirate according to our newly established isolation protocol called subfractionation culturing method, and were evaluated for their efficacy on GVHD treatment, using a mouse MHC-matched B6-->BALB.B GVHD model system. Although the hcMSCs can suppress the allogeneic proliferation of human peripheral blood mononuclear cells in in vitro, the administration of the hcMSCs failed to reduce the GVHD-related mortality of the murine recipients. One of the reasons might be that murine cytokines such as IFN-gamma and TNF-alpha cannot activate the hcMSCs. Based on these results, we suggest that xenogeneic MSCs may not be used for the treatment of GVHD.