Localization of the messenger RNAs encoding three gamma-aminobutyric acid (GABA) transporters, termed GAT-1, GAT-2, and GAT-3, has been carried out in rat brain using radiolabeled oligonucleotide probes and in situ hybridization histochemistry. Hybridization signals for GAT-1 mRNA were observed over many regions of the rat brain, including the retina, olfactory bulb, neocortex, ventral pallidum, hippocampus, and cerebellum. At the microscopic level, this signal appeared to be restricted to neuronal profiles, and the overall distribution of GAT-1 mRNA closely paralleled that seen in other studies with antibodies to GABA. Areas containing hybridization signals for GAT-3 mRNA included the retina, olfactory bulb, subfornical organ, hypothalamus, midline thalamus, and brainstem. In some regions, the hybridization signal for GAT-3 seemed to be preferentially distributed over glial cells, although hybridization signals were also observed over neurons, particularly in the retina and olfactory bulb. Notably, hybridization signal for GAT-3 mRNA was absent from the neocortex and cerebellar cortex, and was very weak in the hippocampus. In contrast to the parenchymal localization obtained for GAT-1 and GAT-3 mRNAs, hybridization signals for GAT-2 mRNA were found only over the leptomeninges (pia and arachnoid). The differential distribution of the three GABA transporters described here suggests that while each plays a role in GABA uptake, they do so via distinct cellular populations.