Given the growing obesity rates among children, a more complete evaluation of their potential cardiometabolic risk is needed. Carotid intima-media thickness (CIMT), a marker of endothelial distress and a predictor of atherosclerotic progression in adulthood, may complete the day-to-day evaluation of children at risk. Multiple risk factors act as additional precipitant causes of atherosclerosis. We analyzed 60 patients aged 6–17 years old by measuring their CIMT using the Aixplorer MACH 30 echography machine automatic measurement software. All subjects were clinically and anamnestically assessed to identify risk factors. CIMT values are significantly higher in older children and boys. Over 20 kg weight gain during pregnancy and other at-risk disorders (p = 0.047), family history of cardiovascular risk (p = 0.049), hypertension (p = 0.012), and smoking (p = 0.015) are linked to increased CIMT. Our study also supports international data on artificial postnatal nutrition, high/low birth weight, and sedentary lifestyle being linked to increased CIMT. Significant correlations were detected between CIMT and the entire lipid panel. Weight excess and abdominal adiposity in children is clearly linked to increased CIMT. Moreover, waist circumference and TG/HDL-c are significant predictors of CIMT. Although each parameter of the lipid panel is correlated to CIMT, fasting glucose is not.