Bulk vacuole isolation, gas chromatography-mass spectrometry, and high-performance liquid chromatography have been used to investigate the accumulation and partitioning of assimilated nitrogen supplied as (NH4Cl)-N-15 between vacuolar and extravacuolar (cytoplasmic) fractions of protoplasts from suspension cultures of carrot (Daucus carota L. cv Chantenay). Glutamine was the most abundant amino acid in the vacuole of protoplasts from late-exponential phase cells, whereas alanine, glutamate, and gamma-aminobutyric acid were located primarily in the cytoplasmic fraction. In N-15-feeding studies, newly synthesized glutamine partitioned strongly to the vacuole, whereas glutamate partitioned strongly to the cytoplasm, gamma-aminobutyric acid was totally excluded from the vacuole, and alanine was distributed in both compartments. Comparison of the N-15-enrichment patterns suggests that initial assimilation to glutamine occurs within a subcompartment of the cytoplasmic fraction. The protoplast-feeding technique may be extended to investigate cytoplasmic compartmentation further.