The flooding dose method, which is used to measure tissue protein synthesis, assumes equilibration of the isotopic labeling between the aminoacyl-tRNA pool and the tissue and blood free amino acid pools. However, this has not been verified for a phenylalanine tracer in an in vivo study. We determined the specific radioactivity of [(3)H]phenylalanine in the aminoacyl-tRNA and the tissue and blood free amino acid pools of skeletal muscle and liver 30 min after administration of a flooding dose of phenylalanine along with [(3)H]phenylalanine. Studies were performed in neonatal pigs in the fasted and refed states and during hyperinsulinemic-euglycemic-amino acid clamps. The results showed that, 30 min after the administration of a flooding dose of phenylalanine, there was equilibration of the specific radioactivity of phenylalanine among the blood, tissue, and tRNA precursor pools. Equilibration of the specific radioactivity of the three precursor pools for protein synthesis occurred in both skeletal muscle and liver. Neither feeding nor insulin status affected the aminoacyl-tRNA specific radioactivity relative to the tissue free amino acid specific radioactivity. The results support the assumption that the tissue free amino acid pool specific radioactivity is a valid measure of the precursor pool specific radioactivity and thus can be used to calculate protein synthesis rates in skeletal muscle and liver when a flooding dose of phenylalanine is administered.