Concentrations of basal and newly synthesized inhibitory (gamma-aminobutyric acid, GABA) and excitatory (glutamate and aspartate) neurotransmitter amino acids and glutamine were determined in mouse brain cortex. Isotopic enrichment following an intravenous infusion of a stable-labeled precursor, [13C6]D-glucose, was used to estimate the newly synthesized amino acid content. Effects of various pharmacological agents (valproate, aminooxyacetic acid, 3-mercaptopropionic acid, N-methyl-D-aspartate, and 2-amino-7-phosphonohepatanoic acid) were evaluated. The effects of 3-mercaptopropionic acid (an inhibitor of glutamate decarboxylase, a GABA-synthesizing enzyme) were restricted to the GABAergic system. On the other hand, N-methyl-D-aspartate (an agonist of a glutamate receptor subtype) was selective for the glutamate-glutamine system, and its effects were prevented by its selective antagonist, 2-amino-7-phosphonoheptanoic acid. In some cases, divergent effects were observed on basal and new amino acids. This suggested that basal and new amino acids may represent different compartments. The anticonvulsant drug valproate caused an increase in basal but a decrease in newly synthesized GABA. Aminooxyacetic acid caused a dramatic increase in basal GABA without affecting the newly synthesized GABA. This approach may be useful in studying compartmentation and fluxes of neurotransmitters.