Positron emission tomography (PET) represents an advanced non-invasive scintigraphic imaging technology and provides a possibility for quantitative characterisation of physiologic processes in human tissues. PET imaging is based on the use of short-lived positron emitting radioisotopes such as carbon-11, oxygen-15 and fluorine-18 and the detection of two photons created in an annihilation reaction between a positron and a tissue electron. PET combined with tracer kinetic models measures blood flow, membrane transport, metabolism, ligand interaction and recently also gene expression non-invasively and quantitatively. Numerous studies on muscle metabolism and perfusion in healthy subjects and in patients with metabolic disorders are conducted to elucidate their regulation and interactions. PET combined with [18F]-2-fluoro-2-deoxy-D-glucose ([18F]FDG) has been widely employed to measure glucose uptake and phosphorylation and muscle and other key organs. In addition, fatty acid uptake and oxidation has been studied. The hybrid PET/CT scanners enable correlation of anatomic and functional information. The sequential scanning procedures including cardiac, hepatic, adipose tissue and cerebral scans are able to give an integrative view of human physiology. Examples of some recent studies on metabolic syndrome and obesity and effects of weight loss are reviewed. Because other methods (e.g. acute exercise and drug interventions, glucose-insulin clamp technique, stable tracer infusions, MRI/MRS) can be combined with PET, it serves an unique tool the assessment of physiology in experimental and clinical settings.