Previous in situ hybridization experiments reported that beta4 (beta 4) neuronal nicotinic acetylcholine receptor (nAChR) transcripts were found only in the medial habenula (MHB). Co-expression in Xenopus oocytes of the beta 4 subunit and any one of three ligand-binding or alpha subunits results in the formation of functional nAChRs. Comparisons between the pharmacology of nAChRs expressed in oocytes and the pharmacology of nAChRs found in the rat CNS prompted a further investigation of the localization of transcripts encoding the beta 4 nAChR subunit. Using two beta 4-specific cRNA probes, in situ hybridization was performed in rat brain. beta 4 mRNA was detected at high levels in the presubiculum, parasubiculum, subiculum and dentate gyrus of the hippocampal formation, in layer IV of the isocortex, in the medial habenula, in the interpeduncular nucleus, and in the trigeminal motor nerve nucleus. Moderate hybridization signals were seen in the isocortex (layers I-III), in olfactory regions, in fields CA1 through CA4 of Ammon's horn and the entorhinal cortex of the hippocampal formation, in the supramammillary nucleus, in the pontine nucleus, in the cerebellum, and in the locus coeruleus. No hybridization above background was detected in the septum, basal ganglia, sensory portions of the brainstem, or spinal cord.