Obesity is associated with a number of risk factors, such as hyperlipidemia, hyperinsulinemia, hypertension, and early atherosclerosis. Evidence indicates that atherosclerosis begins in childhood and progresses over decades. In this work, we examined the relationship between cardiovascular risk factors and ultrasonographic signs of subclinical atherosclerosis in 77 obese children and adolescents compared to 40 non-obese healthy peers. Carotis intima media thickness (cIMT), carotid artery compliance (CAC), brachial artery flow-mediated dilatation (FMD), and established cardiovascular risk factors were studied. In the obese patients, cIMT was significantly increased (0.57 mm vs 0.45 mm, p < 0.001) whereas CAC (1.84% vs 3.29%, p < 0.001) and FMD (9.67 % vs 14.81%, p < 0.001) were significantly decreased. In multiple linear regression analysis, a relation was observed between cIMT, CAC, brachial FMD on one hand, and body mass index (BMI) on the other. Among the lipid anomalies, only hypertriglyceridemia was found to be positively correlated with cIMT. Additionally, we found a significant association between waist circumference (WC) and FMD. These findings indicate that obesity in children is associated with arterial wall alterations and endothelial dysfunction. In hyperlipidemic situations, only hypertriglyceridemia was found to be positively correlated with cIMT. This finding has consistently indicated TG to be a risk factor for the development of atherosclerosis. To our knowledge this is the first study to determine the relation between FMD and WC, which is used as a parameter of obesity in childhood.