We investigated whether body composition, physical activity, physical inactivity, and cardiorespiratory fitness explained the presence of risk factors for cardiovascular disease (CVD) and type 2 diabetes in youth. Eighty-three obese children (6–12 years old) were classified as either low health risk (LHR; n = 30) or high health risk (HHR; n = 53) based on the absence/presence of metabolic risk factors that included measures of dyslipidemia, insulin resistance, and elevated blood pressure. Along with demographic and anthropometric data, body composition, physical activity, physical inactivity, and cardiorespiratory fitness variables were assessed. Risk factor clustering was evident in this sample with 24/83 (29%) possessing at least 2 risk factors. Percent body fat did not differ between the LHR (38.5%) and HHR (39.8%) groups, but total fat mass, total fat-free mass, and central body fat mass were greater in the high health risk group. The strongest predictor for the presence of risk factors was central body fat accumulation. Physical activity, physical inactivity, and cardiorespiratory fitness were unable to predict metabolic risk. Overall, we found that risk factors for CVD and type 2 diabetes were common and that body fat mass and central body fat distribution, in particular, were more important than physical activity, physical inactivity, and cardiorespiratory fitness in predicting metabolic risk in obese children.