Objective To investigate the optimal dosage and timing for 5-bromodeoxyuridine(BrdU) labeling of endothelial progenitor cells(EPCs) from rat circulating blood. Methods The animal model for rat tooth movement was established. EPCs were obtained by density gradient centrifugation. The expressions of specific antigens on cell surface were analysed by immunocytochemistry and fluorescenceochemistry. EPCs were incubated with BrdU at different concentrations(5, 10, 15 μmol/L) for different incubating time(12, 24, 48, 72, 96 h) to identify the optimal BrdU concentration and incubating time for cell labeling. Immunohistochemistry was performed to calculate the labeling index(LI). Results The culture cell positively expressed CD34, CD133 and could be shown to endocytose DiIac- LDL, FITC-UEA-1. Incubation of the EPCs with BrdU at 10 μmol/L and for an optimal length of 72 h appeared to achieve the highest LI(66.8±2.9)%, which was significantly higher than group of 5 μmol/L(P<0.05), while there was no significant difference between the group of 15 μmol/L and 10 μmol/L(P>0.05). Conclusion EPCs can be isolated from tooth movement rat circulating blood and cultured. Incubation of the EPCs with BrdU at 10 μmol/L and for an optimal length of 72 h appeared to achieve the optimal LI. This provides a foundation for us to investigate the mechanism of chemiotaxis and differentiation for EPCs.