The quantitative significance of amino acids to plant nutrition remains controversial. This experiment determined whether post-uptake metabolism and root to shoot export differ between glycine and glutamine, and examined implications for estimation of amino acid uptake. Field soil containing a Eucalyptus pauciflora seedling was injected with uniformly 13C- and 15N-labelled glycine or glutamine. I quantified 15N and 13C excess in leaves and roots and intact labelled amino acids in leaves, roots and stem xylem sap. A tunable diode laser quantified fluxes of 12CO2 and 13CO2 from leaves and soil. 60360 min after addition of amino acid, intact molecules of U-13C,15N glutamine were < 5% of 15N excess in roots, whereas U-13C,15N glycine was 30100% of 15N excess in roots. Intact molecules of glutamine, but not glycine, were exported from roots to shoots. Post-uptake metabolism and transport complicate interpretation of isotope labelling such that root and shoot contents of intact amino acid, 13C and 15N may not reflect rates of uptake. Future experiments should focus on reconciling discrepancies between intact amino acid, 13C and 15N by determining the turnover of amino acids within roots. Alternatively, post-uptake metabolism and transport could be minimized by harvesting plants within minutes of isotope addition.