Background and aims: Radioactive and stable amino acid isotopes are frequently used in metabolic research. Blood cells contain amino acid transporters, which may influence tracer distribution in blood. The aim of this study was to determine whether plasma or whole blood specific activity or enrichment of amino acid tracers should be used in the calculation of whole body and organ production rates. Methods: Seven male Wistar rats were infused with L-[2,3-H-3]-Arginine, L-[2,6-H-3]-Phenylalanine, L-[3,4-H-3]-Valine, and [L-[4,5-H-3]-Leucine, Whole body and portal drained visceral, hepatic and renal production rates of arginine, phenylalanine, valine and leucine were determined in plasma and in whole blood. Results: Amino acid tracers that equilibrate well between plasma and blood cells (for instance phenylalanine, valine and leucine) yield similar whole body production rates when whole blood or plasma is sampled. Also, organ production rates measured using these amino acid tracers are consistent. However, a discrepancy exists between the whole body production rate and the sum of PDV, hepatic and renal production rates. When tracers are used that do not equilibrate well between plasma and blood cells (for instance arginine) the use of whole blood specific activity in the calculations yield overestimations of whole body and organ production rates. Conclusion: From our data we recommend plasma sampling and strongly advise against whole blood sampling in metabolic organ balance studies in which amino acid tracers are used.