Objective To investigate the influencing factors of endothelial dysfunction in patients with non-obstructive coronary atherosclerosis. Methods A total of 110 consecutive patients with suspected coronary artery diseases and then diagnosed with non-obstructive coronary atherosclerosis (coronary stenosis <50%) by coronary angiography in Xuanwu Hospital, Capital Medical University from June 2013 to June 2015 were recruited in this study. Flow mediated dilatation (FMD) was measured by echocardiography, and circulating endothelial progenitor cells (EPCs) were enumerated by flow cytometry as mononuclear cells expressing a combination of KDR⁺, CD34⁺ and/or CD133⁺. The patients were divided into control (FMD >10%) and endothelial dysfunction group (FMD ≤10%). SPSS statistics 19.0 was used to perform the statistical analysis. Logistic regression analysis was employed to analyze the influencing factors for endothelial dysfunction. Results There were no significant differences in the cell counts of circulating EPCs, defined as CD34⁺/KDR⁺,CD133⁺/KDR⁺ or CD34⁺/CD133⁺/KDR⁺ cells between the 2 groups (P>0.05). Logistic regression analysis revealed that age was an independent risk factor for endothelial dysfunction (95%CI 1.004-1.104, P=0.033). Conclusion Age, not the count of circulating EPCs, is an independent influencing factor of endothelial dysfunction in patients with non-obstructive cornary atherosclerosis.