The application of advanced methods and techniques and their continuous development enable detailed body composition analyses (BCAs) and modeling of body composition at different levels (e.g., at atomic, molecular, organ-tissue and whole body level). Functional body composition integrates body components into regulatory systems (e.g., on energy balance). Regulation of body weight is closely linked to the mass and function of individual body components. Fat mass is part of the energy intake regulatory feedback system. In addition, fat-free mass (FFM) and fat mass are both determinants of resting energy expenditure (REE). Up to 80% of the variance in energy intake and energy expenditure is explained by body composition. A deviation from normal associations between body components and function suggests a metabolic disequilibrium (e.g., in the REE-FFM relationship or in the plasma leptin-fat mass association) that may occur in response to weight changes and diseases. The concept of functional body composition adds to a more sophisticated view on nutritional status and diseases, as well as to a characterization of biomedical traits that will provide functional evidence relating genetic variants.