The localization of GABA transporters (GAT1 and GAT3) was examined immunocytochemically in the rat cerebellum at both light and electron microscopic levels using antibodies specific for each subtype. Immunoblot analysis showed that the antibodies against GAT1 and GAT3 specifically recognized their respective antigens in the cerebellum. Both GAT1 and GAT3 were found in the neuropil but not in neuronal somata or glial cell bodies. GAT1 immunoreactivity was seen throughout all layers of the cerebellar cortex with the highest immunoreactivity in the molecular layer, but little immunoreactivity was found in the deep cerebellar nuclei. GAT1 immunoreactivity was seen in the pinceau area of the Purkinje cell layer and in the mossy fiber glomeruli in addition to the neuropil of the molecular layer. Weak GAT3 immunoreactivity was found in the granular layer of the cerebellar cortex, and intense immunoreactivity was observed around the unstained large neurons in the deep cerebellar nuclei. Electron microscopic analysis of the cerebellum revealed that GAT1 immunoreactivity was predominantly localized in the presynaptic terminals, while GAT3 immunoreactivity was localized in the glial processes. These results suggested that GABAergic transmission at synapses is terminated by three GABA uptake systems, (1) only neuronal uptake through GAT1, (2) only glial uptake through GAT3, and (3) both neuronal and glial uptake through GAT1 and GAT3 respectively, and also that the GABA uptake system is different in each type of GABAergic neuron.