The impact of body composition on the early origin of chronic diseases is an increasingly appreciated phenomenon. Little is known about the characteristics of children with varying body composition. The aim of this study was to investigate serum lipid profiles and other characteristics in relation to body composition. The data of 1394 participants (aged 6 to <18 years) of the observational general population-based Austrian LEAD Study have been analyzed. Body composition groups were defined by appendicular lean mass (ALMI) and fat mass (FMI) indices assessed by DXA. Serum lipid profiles (triglycerides, LDL-c, HDL-c) and other characteristics (e.g., prematurity, smoke exposure, physical activity, nutrition) were investigated in these body composition groups. Different body composition groups, which are not distinguishable by BMI, exist. Children with high ALMI and high FMI showed higher triglycerides and LDL-c, but lower HDL-c levels. In contrast, levels did not differ between those with high FMI but low (or normal) ALMI, and other body composition groups. BMI should be interpreted cautiously, and body composition should be measured by more precise techniques. In particular, children and adolescents with high FMI who have concomitantly high ALMI should be followed closely in future studies to investigate whether they are at increased risk of cardiovascular problems.