We aimed to measure flow-mediated dilation (FMD), carotid intima-media thickness (cIMT), and to evaluate the effects of waist circumference (WC), and body mass index Z (BMI-Z) score on these parameters in obese children. This case-control cross-sectional study included 70 obese and 40 non-obese children aged 7-14 years who presented with various complaints and had no concomitant diseases. FMD and cIMT were measured in all subjects and correlated with anthropometric and biochemical factors. WC, BMI-Z score, systolic and diastolic blood pressure (BP), triglyceride (TG) and insulin concentrations, and homeostatic model assessment (HOMA) index were significantly higher, whereas high density lipoprotein (HDL) -cholesterol concentration was significantly lower in the obese than in the non-obese group. FMD values were significantly lower, whereas cIMT values were significantly higher in obese than in non-obese subjects. FMD negatively correlated with WC, BMI-Z score, serum insulin level, HOMA, systolic BP, triglyceride but positively with HDL-cholesterol. cIMT positively correlated with WC, BMI-Z score, serum insulin level, HOMA, systolic BP, triglyceride but negatively with HDL-cholesterol. Increased WC, BMI-Z score, serum insulin level, HOMA, systolic BP, triglyceride and decreased HDL-cholesterol in obese children contribute to endothelial dysfunction and early subclinical atherosclerosis compared to their normal weight peers.