The expression of mRNAs encoding different beta subunits (beta 1, beta 2, and beta 3) of the gamma-aminobutyric acid A (GABAA) receptor in the rat brain was investigated by in situ hybridization histochemistry. Transcripts of each subunit showed region-specific localization. Some areas contained all three beta subunit mRNAs, while other areas showed marked differences in the location and level of expression of each subunit mRNA. The regions with strong to very strong labeling by the beta 3 probe were as follows: the olfactory bulb, the cortex, the caudate-putamen, the accumbens nucleus, the hypothalamus, the amygdala, the hippocampal formation, and some areas of the brainstem and spinal cord. Weak to moderate labeling was detected in the thalamus, superior and inferior colliculus, and many areas of the brainstem. The regions with strong to very strong labeling by the beta 2 probe were as follows: the olfactory bulb, the ventral pallidum, the globus pallidus, the nucleus of the diagonal band, the preoptic magnocellular nucleus, the thalamus, the subthalamic nucleus, the substantia nigra, and the cerebellum. Weak to moderate labeling was detected in the regions that showed strong expression of beta 3 subunit mRNA. Expression of beta 1 subunit mRNA was only weak to moderate compared to that of the beta 2 and beta 3 subunit mRNAs. The regions with moderate labeling by the beta 1 probe were the following: the cortex, the claustrum, the bed nucleus of the stria terminale, some nuclei of thalamus and amygdala, the hypothalamus, the hippocampal formation, the subiculum, the cerebellum, and several areas of the brainstem and spinal cord. Thus, our findings showed that the beta subunit mRNAs of the GABAA receptor were differentially expressed in the rat brain, perhaps indicating the existence of different subtypes of the GABAA receptor in different brain regions.