Amino acids labeled with 13C or deuterium are commonly used in studies of amino acid metabolism. Traditionally, amino acid flux has been estimated by measurement of isotopic enrichment in the plasma pool; however, urine sampling as a noninvasive means of determining isotope enrichment has been increasing. The isotope enrichments and fluxes estimated from plasma and urine sampling were compared when two phenylalanine tracers (L-[1-13C]phenylalanine and L-[ring-2H5]phenylalanine) were intravenously infused for 4 hours in seven healthy men. This is the first evaluation of these isotopes as urinary tracers for assessing amino acid metabolism in adult humans. Before infusion, the mean ratio of plasma to urine (P:U) isotope enrichment was 0.99 +/- 0.03 (SD) and 0.99 +/- 0.02 for [13C]phenylalanine and [13C]tyrosine, respectively (isotope enrichment of [2H5]phenylalanine is zero at baseline). At isotopic steady state, the ratio was 1.06 +/- 0.05, 0.98 +/- 0.03, and 0.60 +/- 0.10 for [13C]phenylalanine, [13C]tyrosine, and [2H5]phenylalanine, respectively. The [13C]phenylalanine isotope showed a high correlation (R2 = .96) between enrichment in plasma and urine. However, use of [2H5]phenylalanine resulted in a significantly higher enrichment in urine than in plasma. Since amino acid flux is inversely related to enrichment, urine sampling would result in an underestimation of flux. The plasma to urine difference is probably due to discrimination of the [2H5]phenylalanine isotope in renal transport; therefore, this isotope may not be suitable for in vivo use where cellular transport mechanisms are involved.