Data have shown that circulating endothelial progenitor cells (EPCs) closely correlate with the vascular endothelial layer state. The present study was designed to describe the evolution of EPCs in children before and 24 h after transcatheter closure surgery for occluding congenital heart disease. Three groups of patients were studied: the transcatheter closure of atrial septal defect (ASD) group (group 1), the transcatheter closure of patent ductus arteriosus (PDA) group (group 2), and the transcatheter closure of ventricular septal defect (VSD) group (group 3). The circulating EPC level was detected using flow cytometry measuring CD34 and kinase insert receptor double-positive mononuclear cells. The concentration of vascular endothelial growth factor (VEGF) was assessed by enzyme-linked immunosorbent assay. The fluoroscopy time was correctly recorded during the surgery. All of the data were collected before and 24 h after surgery. EPC level and VEGF concentration did not change significantly before and at 24 h after surgery in groups 1 and 2. In group 3, the level of circulating EPCs and VEGF concentration increased significantly 24 h after surgery. The fluoroscopy time in group 3 was significantly longer than in groups 1 and 2. The increased volume of EPCs and VEGF were positively correlated in group 3. Our results showed that transcatheter closure of PDA and ASD in children does not lead to increased circulating level of EPCs. Transcatheter closure of VSD may result in vascular endothelium injury as indicated by increased circulating EPC level.