Background: To investigate endothelial dysfunction and morphological vascular changes in childhood obesity. Methods: 93 overweight/obese children (body mass index 26 ± 5 kg/m2; median 26 kg/m2; interquartile range 22–28 kg/m2), mean age 10.9 ± 2.7 years, underwent a check-up of total, high-density lipoprotein- and low-density lipoprotein-cholesterol, triglycerides, C-reactive protein, erythrocyte sedimentation rate, and white blood cell count, together with ultrasound measures of flow-mediated dilatation, carotid intima-media thickness, and anterior-posterior diameter of the abdominal aorta. Results: The body mass index of overweight/obese children had a statistically significant linear relationship ( p < 0.05) with triglycerides, erythrocyte sedimentation rate, carotid intima-media thickness, anterior-posterior diameter of the abdominal aorta, and flow-mediated dilatation values. Conclusions: Overweight/obese children have an initial endothelial dysfunction and vascular damage, i.e., the first stage in the development of atherosclerosis.