The aim of this study was to assess the relationship between cystatin C (CysC), cardiometabolic risk factors (CMRFs), and body composition in severely obese children. We evaluated 117 children aged 7-14 years old. Seventy-nine of these were severely obese (body mass index z-score ranging from 2.1 to 8.4), and 38 were children with normal nutrition state. CysC was determined by immunonephelometry. CMRFs (glucose, insulin, high-density lipoprotein cholesterol, triglycerides, homocysteine, uric acid, alanine aminotransferase, and high-sensitivity C-reactive protein) were measured by standard biochemical methods. Blood pressure was evaluated at the clinical examination. Renal function was estimated using the glomerular filtration rate (eGFR) based upon creatinine levels, and body weight (Léger formula). Body composition was assessed by segmental bioelectrical impedance. Obese children at the highest tertile of CysC values were characterized by their aggregation of CMRFs. CysC concentration was associated with insulin resistance, alanine aminotransferase, uric acid, and homocysteine after adjusting for age, gender, and eGFR. CysC values were also correlated with the fat-free mass and specifically with skeletal muscle mass. CysC levels were correlated with CMRFs factors independently of renal function, and affected by skeletal muscle mass in severely obese children, although they are less influenced by this than is creatinine.