The present provides a Positional Isotopomer NMR Tracer Analysis (PINTA) method that can be used to noninvasively assess rates of hepatic mitochondrial oxidation (VCS) and/or pyruvate carboxylase (VPC) flux in a subject. In certain embodiments, the methods utilize a combined NMR/gas chromatography-mass spectrometry analysis of plasma following infusion of [3-13C]lactate and glucose tracer. The method of the invention provides investigators with a tool to non-invasively examine the role of altered hepatic mitochondrial metabolism and study the effects of therapeutic interventions for the treatment of non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and type 2 diabetes (T2D).