Profiling of metabolic states requires that an enormous amount of information be known about the system in question. Frequently the volume of data that can be derived from a source must be weighed against the relevance of the model used to obtain it. Organ-scale analysis presents such a modeling conundrum; the liver in particular would be an enormously beneficial system to characterize but no studies to date have successfully described its in vivo metabolic state. To address this issue, we used a combination of empirical measurements and mathematical modeling (a mass balance technique using stoichiometry: Metabolic Flux Analysis (MFA)) to derive the remaining unknowns. A novel protocol has been developed with which we were able to measure the in vivo flow rates and plasma concentrations of over 19 metabolites and 20 amino acids, as well as perform a complete blood gas analysis, across the hepatic vasculature of rats (n=30). Normal (sham) fasted rats were compared to rats that received either 20% or 40% total body surface area burns; clustering revealed that there were significant differences between the groups of measured metabolites. Analysis of the concentrations at the portal vein, hepatic artery and suprahepatic vena cava (isolated to drain only hepatic veins) revealed elevated glucose, insulin, cholesterol and circulating amino acids in the 40%B group; entirely consistent with the clinical features of the hypermetabolic response observed in burn-injured humans. MFA was performed per rat and the conversion of concentrations to fluxes intimated a possible homeostatic mechanism by which the net elevated flow rates in burn rats (40% rise in 40%B rats compared to sham) largely reduced the disparity in concentration levels for certain metabolites. The data revealed that the liver responds to concentrations and influxes in three primary ways: 1) It is highly sensitive to certain metabolites and will return them to the normal efflux values regardless of the size of the influx e.g. ammonia, oxygen and alanine were of lower concentrations in burn animals, but the fluxes in this group showed higher uptake rates and reduced efflux values to sham levels. 2) It is responsive to fluxes rather than concentrations for some metabolites e.g. reduced circulating concentrations of albumin, lactate and glutamate in burn groups appeared as normal influxes and the liver did not attempt to change the efflux to restore concentrations to normal. 3) The opposite trend can also be observed as in the cases of glucose, BUN and cholesterol, where the concentrations and subsequently fluxes, were much higher but the uptake/output by the liver remained constant. Metabolic flux analysis shows the adjustments in intermediary metabolites within the liver that accommodate the unusual cases of increased fluxes with normal uptake, and the reduction of certain fluxes to a floor-level. This data provides unique insight into the physiology of the liver and its attempts to restore homeostasis post-trauma. This protocol provides us with a unique tool to compare differing metabolic states at an organ scale and is an invaluable reference for further design of physiologically relevant bioartificial or tissue engineered constructs.