The investigation of protein metabolism under various nutritional and physiological conditions has been made possible by the use of indirect, principally tracer-based methods. Most studies were conducted at the whole-body level, mainly using steady-state isotopic techniques and equations based on simple two-pool models, in which amino acids are either free or protein bound. Because whole-body methods disregard regional contributions to protein metabolism, some regional approaches have tried to distinguish the distribution of protein kinetics in the different tissues. The organ-balance tracer technique, involving the arteriovenous catheterization of regions or organs with concomitant isotopic tracer infusion, distinguishes between amino acid uptake and release in the net amino acid balance and measures protein synthesis and degradation under steady-state conditions. Last, the importance has become clear of the difference in dietary and endogenous amino acids recycled from proteolysis for anabolic and catabolic pathways. In humans, the dual tracer technique, which consists of the simultaneous oral/enteral administration and intravenous infusion of different tracers of the same amino acid, allows an estimate of the splanchnic uptake of amino acids administered. Furthermore, the whole-body retention of labeled dietary nitrogen after the ingestion of a single protein meal has enabled a clearer understanding of the metabolic fate of dietary amino acids. Based on such data, a newly developed compartmental model provides a simulation of the regional distribution and metabolism of ingested nitrogen in the fed state by determining its dynamic fate through free and protein-bound amino acids in both the splanchnic and peripheral areas in humans.