Iron overload can affect cardiac structure and function by the production of free radicals in addition to iron deposits in heart muscle. The purpose of this study was to compare traditional and non-traditional cardiovascular risk factors (CVRF) in children and adolescents on renal replacement with and without iron overload. Also, we evaluated the relationships between iron overload and left ventricular mass (LVM). First, in a cross-sectional study, we evaluated traditional and non-traditional CVRF in 143 children and adolescents, 48 on peritoneal dialysis (PD), 53 on hemodialysis (HD) and 42 after renal transplantation according to iron overload. In a second phase with a case-control study, we measured LVM in 12 case patients and 12 matched controls. Iron overload was identified in 15 patients (10.5%), 11 in HD and 4 in PD (P = 0.002). The group with iron overload had lower body mass index (17 versus 19; P = 0.01), total cholesterol (132 versus 165 mg/dL; P = 0.03) and hemoglobin (8.5 versus 10.6 g/dL; P = 0.003) but higher interleukin (IL)-6 levels (4.8 versus 3.6 ng/L; P = 0.04) and hypertension diagnosis (79 versus 48%; P < 0.001) than those without iron overload. Ferritin showed a positive correlation with C-reactive protein (CRP) and IL-6 levels. In a subgroup of 24 patients (12 with and 12 without iron overload), LVM was not different. However, ferritin levels showed a borderline positive correlation (r = 0.44, P = 0.05) with LVM. Children and adolescents with iron overload show more CVRFs, especially if they received replacement therapy with HD. Ferritin is related to CRP and IL-6 levels.