Functional abnormalities of the endothelial system may be caused by allogeneic hematopoietic stem cell transplantation (HSCT). The aim of this study is to explore the possibility that endothelial progenitor cells (EPCs) can be used in endothelial repair post-HSCT. EPCs were isolated from mouse bone marrow by density centrifugation and differential adherence. Numbers of endothelial cells (ECs) (CD31(+)CD133(-)CD45(-)), EPCs (CD31(+)CD133(+)-CD45(low/-)) and carboxyfluorescein succinimidyl ester (CFSE)-positive cells in peripheral blood, spleen and bone marrow were determined at various time points by flow cytometry. The distribution of labeled EPCs was observed by fluorescence microscopy; morphological alterations of tissues were assessed by light microscopy and transmission electron microscopy. In the irradiated group, the numbers of circulating ECs and EPCs were elevated after pre-conditioning, reaching peaks at days 3 and 5; the counts remained high for about 5 days. In addition, CFSE-labeled cells were visualized in tissue and bone marrow. In conclusion, these results suggest the following: (a) the EPCs derived from mouse bone marrow mononuclear cells express phenotypes characteristic of normal EPCs, (b) irradiation during preconditioning damaged the endothelium, which initiated mobilization of EPCs, and (c) injury to the endothelium also caused extrinsic EPCs home to the damaged tissue.