Glutamate is an important neurotransmitter in the circuitry of the basal ganglia. Of the four pharmacological classes of receptors that may mediate the actions of glutamate, the N-methyl-D-aspartate (NMDA) type is of particular interest insofar as it has been implicated in the neural processes underlying long-term synaptic plasticity as well as excitotoxic injury. NMDA ligand binding sites are abundant in the structures of the basal ganglia, and NMDA receptors have been linked to neuronal excitability, neuropeptide gene expression, and regulation of dopamine release in these regions. NMDA receptors are believed to be heterooligomers of subunits from two families: NMDAR1, encoded by a single gene but alternatively spliced to produce eight distinct isoforms (NMDAR1A-H), and NMDAR2, encoded by four separate genes (NMDAR2A-D). We have used in situ hybridization with a total of 13 oligonucleotide probes to examine the expression of these genes in the rat basal ganglia. NMDAR1 subunits are expressed throughout the basal ganglia as well as in the rest of the brain; however, the alternatively spliced amino-terminal region Insertion I is abundantly expressed only in the subthalamic nucleus and is not detectable in the neostriatum, globus pallidus, or substantia nigra pars compacta. In contrast, expression of the carboxy terminus segment Deletion I is prominent in the striatum but is not observed in other elements of the basal ganglia. NMDAR2 subunits also exhibit differential expression: NMDAR2B is abundant in the striatum, but NMDAR2A is present within the striatum only at low levels. NMDAR2C is present in the substantia nigra pars compacta only, while NMDAR2D exhibits an unusual distribution, with high levels of expression in the substantia nigra pars compacta, the subthalamic nucleus, the globus pallidus, and the ventral pallidum. Since each isoform of the NMDAR1 and NMDAR2 subunits can confer distinct properties on the resultant NMDA receptor, these data imply that there is a high degree of regional specialization in the properties of NMDA receptors within the basal ganglia.