Aim: To investigate endothelial progenitor cells level and ultrasound measurements of arterial function: flow-mediated dilation and carotid artery stiffness index in the convalescence of Kawasaki disease. Methods: 63 children were studied, divided into coronary artery lesion group (Group1, n=21), non-coronary artery lesion group (Group2, n=20), and control group (Group3, n=22). Endothelial progenitor cells count and arterial function were measured by flow cytometry analysis and by ultrasound respectively. Results: Flow-mediated dilation in three groups were 4.5%±1.5%, 9.5%±2.8% and 12.1%±2.3% (Group1 vs Group2, Group1 vs Group3, Group2 vs Group3, all p<0.01), Carotid artery stiffness index were 4.10±0.44, 3.81±0.50 and 3.59±0.46 (Group1 vs Group2, p<0.05; Group1 vs Group3, p<0.01; Group2 vs Group3, p=0.142) and the number of endothelial progenitor cells were 2.0±0.6/ul, 4.2±0.8/ul, 4.5±0.7/ul (Group1 vs Group2, p<0.01; Group1 vs Group3, p<0.01; Group2 vs Group3, p=0.292). Multiple linear regressions identified flow-mediated dilation and carotid artery stiffness index as significant determinants of endothelial progenitor cells level. Endothelial progenitor cells level had significant correlations with flow-mediated dilation and carotid artery stiffness index by Pearson correlation analysis. Conclusion: Our findings suggest that systemic arterial dysfunction persist in the convalescence of Kawasaki disease. The level of endothelial progenitor cells could serve as a surrogate biologic measurement of vascular function.