Children with acquired and congenital heart disease (CHD) are increasingly surviving to adulthood. Our aim was to determine the prevalence of coronary artery disease (CAD) risk factors in children at known risk for early CAD or with severe CHD. We recruited children (8–19 years) at risk for early CAD—Kawasaki disease (KD, N = 36) and coarctation (69) or severe CHD: > 1 cardiopulmonary bypass surgery (60), single ventricle (15), prosthetic valves (13). Anthropometric measurements, blood pressure, and fasting lipid data were compared with summaries from National Health and Nutrition Examination Survey (NHANES) publications (1999–2012). Relative risk (RR) ratios were calculated based on age classification and pooled to obtain overall RR. Of 174 subjects, 106 were male (61%) and 138 (79%) had CHD. Compared to NHANES data, hypertension and low HDL were higher in the study cohort [RR 11.7 (CI 6.34–21.6), p < 0.001; and 1.79 (CI 1.36–2.35). p < 0.001] and obesity and elevated total cholesterol were lower [RR 0.59 (CI 0.37–0.96), p = 0.03; and 0.42 (CI 0.19–0.95), p = 0.04]. Elevated non-HDL was similar between groups. Age category had similar RR for all CAD risk factors. Eight subjects had metabolic syndrome. Risk factors were similar between KD versus CHD subgroups. Both coarctation and non-coarctation subjects had increased RR for hypertension. Hypertension is the most common risk factor for children at risk of early CAD and severe CHD. Metabolic syndrome is rare. These patients should be screened and treated for hypertension and current recommendations for universal lipid screening are adequate for follow-up.