The aim of study was to investigate the injury of bone marrow microenvironment after γ ray irradiation conditioning in mouse allogeneic hematopoietic stem cell transplantation (allo-HSCT). The mononuclear cells collected from mice bone marrow for culture in vitro, were identified by flow cytometry with double staining when cultured for 5 - 7 days. Mice were separated randomly into 4 groups, namely, the control group, irradiation group, endothelial progenitor cell (EPC) transplantation group and irradiation combined EPC transplantation group. Peripheral blood was collected to assay the circulating white blood cells. The histological, electron microscopic and immunofluorescence analyses of bone marrow were performed in the same time, furthermore the distribution of labeled EPC was determined. The results showed that EPC were identified as CD45(low/-)CD133(+)CD31(+), double positive of Dil-Ac-LDL and FITC-UEA-1. The bone marrow microenvironment injury of recipient mice was shown in the irradiation group in which the number of WBC began to decrease after conditioning, and the mice were all died at 8 days (p < 0.05). The intramedullary hemorrhage could be detected by light microscopy at 3 days after irradiation, when the destruction of connection between endothelial cell and the basement membrane was observed by TEM. There were CFSE labeled cells in bone marrow in irradiation combined EPC transplantation group at 18 hours after transplanted cultured EPC in vitro, the number of CFSE(+) cells was 58-folds of EPC transplantation group (p < 0.05). It is concluded that the irradiation can cause the severe endothelium injury that drives extrinsic EPC homing to the injured bone marrow microenvironment.