We investigated the composition of free amino acids in walnut (Juglans regia L.) seeds (embryo and cotyledons). We also examined xylem transport of free amino acids in young seedlings grown in the absence of external nutrients. A relatively high concentration of free alanine was found in seed tissue, whereas a relatively high concentration of citrulline was detected in young seedlings. Citrulline was the main free amino acid transported in the xylem to stem and leaves. The negligible presence of citrulline, a non-protein amino acid, in the kernel and its presence in high concentrations in all of the tissues of young seedlings, including cotyledons, embryonic axis, taproot and stem, suggest that citrulline is synthesized during walnut germination. We conclude that citrulline plays an important role in nitrogen translocation during walnut germination.