The cellular localization of transcripts for a new putative agonist-binding subunit of the neuronal nicotinic acetylcholine receptor (nAChR), alpha 5, was examined using in situ hybridization in the rat central nervous system (CNS), alpha 5 subunit mRNA was localized to a small number of regions when compared with two of the other known agonist-binding subunits, alpha 3 and alpha 4, alpha 5 mRNA is expressed at relatively high levels in neurons of the subiculum (pyramidal layer), presubiculum and parasubiculum (layers IV and VI), which are components of the hippocampal formation, in the substantia nigra pars compacta and ventral tegmental area, in the interpeduncular nucleus, and in the dorsal motor nucleus of the vagus nerve. Moderate hybridization signals were detected in neurons of the isocortex (layer VIb), anterior olfactory nucleus, trigeminal ganglion, superior olivary complex, nucleus of the solitary tract, and area postrema. No hybridization above background levels was seen in the amygdala, septum, thalamus, hypothalamus, or cerebellum. These results suggest that the alpha 5 subunit differs from other known agonist-binding subunits in its distribution.