Abstract: Objective To observe the differentiation and migration of SCA1^-/CD31^- cardiac side population (CSP) cells in mice and their mechanisms. Methods CSP cells were separated by fluorescence activated cell sorting (flow cytometry), and SCA1^-/CD31^-CSP cells marked by PKH26 were injected into myocardium in the mice model of myocardial infarction (MI). The migration and localization of these cells were observed. Differentiation of cells and the expression levels of E-cad were detected by tissue staining and reverse transcriptase PCR; The effect of SDF-1α/CXCR4 pathway was detected by chemotaxis assay. Results SCA1^-/CD31^-CSP cells could migrated to ischemia area from the puncture site, and fluorescent markers showed that they had differentiated into endothelial cells and vascular structure. Compared with control group, the expression of E-cad in SCA1^-/CD31^- CSP cells decreased significantly after MI; the migration induced by SDF-1α was obviously dose-dependent and could be blocked by CXCR4 antibody. Conclusion SCA1^-/CD31^- CSP cells in the mice heart can be used as endothelial progenitor cells. SDF-1α/CXCR4 pathway may play an important role in migration of these cells.