A novel anti-β3 subunit-specific GABAA receptor (GABAAR) antibody has been prepared by immunizing a rabbit with a bacterial fusion protein of the large intracellular loop of the β3 subunit. The antiserum immunoprecipitated the solubilized GABAA receptor. The anti-β3 antibody was affinity purified on immobilized β3 large intracellular loop peptide. In immunoblots, the purified antibody reacted with a 57 KDa peptide. Immunocytochemistry with the affinity-purified antibody has revealed the localization of the β3 subunit in the rat brain. A comparative study with the immunocytochemical distribution of the β2 subunit has also been performed. There are areas of the brain and cell types where the distribution of β2 and β3 overlap (i.e., cerebral cortex, cerebellum,and most layers of the olfactory bulb). There are also clear differences in the expression of β3 and β2 in other brain areas and cell types. Thus, high β3 but low or no β2 expression was observed in the corpus striatum and in granule cells of the olfactory bulb. In the hippocampus the expression of β3 was considerably higher than that of β2, but some hippocampal interneurons showed high expression of β2. High β2 but little or no expression of β3 was observed in thalamic nuclei, substantia nigra, globus pallidus, inferior colliculus and the short axon cells of the olfactory bulb. J. Comp. Neurol. 413:535–548, 1999. © 1999 Wiley-Liss, Inc.