Although abnormal glucose metabolism defines type 2 diabetes mellitus (T2DM), efforts to understand the pathogenesis of T2DM are increasingly focused on disordered lipid metabolism. Magnetic resonance spectroscopy (MRS) is a non-invasive technique which provides real time data. Its uses in metabolic studies include: 1) static measurements of energy stores e.g. intramyocellular and hepatic glycogen and triglyceride levels and, 2) dynamic measures of mitochondrial function (ATP synthesis and TCA cycle flux). Studies utilizing these techniques have already provided several novel insights into the pathogenesis of type 2 diabetes and other metabolic disorders. Recent work exploring the mechanistic links between disorders of fatty acid/lipid metabolism and insulin resistance will be discussed. Studies examining energy balance in thyroid hormone resistance will also be briefly reviewed.