In this study, we aimed to analyze early-onset atherosclerotic changes in adolescents with risk of cardiovascular disease in comparison to healthy controls using carotid intima media thickness (CIMT), homocysteine and markers of endothelial function as indicators. Children aged 10 years or older, all pubertal, with type 1 diabetes mellitus (T1DM), obesity, or obesity with glucose intolerance and age- and sex-matched healthy controls were included in the study. Endothelial markers (von Willebrand factor [vWF], tissue plasminogen activator [tPA], plasminogen activator inhibitor [PAI]-1), CIMT, homocysteine, folic acid, and vitamin B12 levels were measured in all subjects. Mean CIMT of the obese subjects were significantly higher than that of lean diabetic children and healthy controls (p=0.024). There was an independent relationship between CIMT and homocysteine level (b=0.76, p<0.0001). Further, homocysteine was negatively correlated with vitamin B12 (r=-0.20, p<0.001) and folic acid (r=-0.44, p<0.001). Homocysteine is an independent risk factor for early atherosclerosis in adolescents, which may be controlled by supplementation with vitamin B12 and folic acid.