The predominant nicotinic acetylcholine receptor (nAChR) subtype in brain binds nicotine with high affinity and has an alpha 4:beta 2 subunit stoichiometry of 2:3. In this study, the mRNA levels of nAChR alpha 4 and beta 2 subunits were simultaneously quantitated by ribonuclease protection assay and compared with the number of alpha 4 beta 2 receptor subtype, measured by (-)-[3H]nicotine binding in the cerebellum, brain stem, hippocampus, cortex, thalamus and striatum of rat brain. The rank order of abundance of alpha 4 and beta 2 mRNA was different from that of alpha 4 beta 2 receptor subtype levels in the six brain regions studied. The ratio of alpha 4:beta 2 transcripts varied from 2:2.6 to 2:33 in these brain regions. These results reveal a differential co-expression of alpha 4 and beta 2 subunit genes in various regions of rat brain.