Any given subunit of the heteromultimeric type-A gamma-aminobutyric acid (GABA) GABA(A) receptor may be present in several receptor subtypes expressed by individual neurons. Changes in the expression of a subunit may result in differential changes in the expression of other subunits depending on the subunit composition of the receptor subtype, leading to alterations in neuronal responsiveness to GABA. We used the targeted disruption of the alpha 6 subunit gene to test for changes in the expression of other GABA(A) receptor subunits. Immunoprecipitation and ligand binding experiments indicated that GABA(A) receptors were reduced by approximate to 50% in the cerebellum of alpha 6-/- mice. Western blot experiments indicated that the alpha 6 subunit protein completely disappeared from the cerebellum of alpha 6-/- mice, which resulted in the disappearance of the delta subunit from the plasma membrane of granule cells. The amount of beta 2, beta 3 and gamma 2 subunits was reduced by approximate to 50%, 20% and 40%, respectively, in the cerebella of alpha 6-/- mice. A comparison of the reduction in the level of alpha 1, beta 2, beta 3, gamma 2, or delta-subunit-containing receptors in alpha 6-/- cerebellum with those observed after removal of alpha 6-subunit-containing receptors from the cerebella of alpha 6+/+ mice by immune-affinity chromatography demonstrated the presence of a significantly higher than expected proportion of receptors containing beta 3 subunits in alpha 6-/- mice. The receptors containing alpha 1, beta 2, beta 3 and gamma 2 subunits were present in the plasma membrane of granule cells of alpha 6-/- mice at both synaptic and extrasynaptic sites, as shown by electron microscopic immunocytochemistry. Despite the changes, the alpha 1 subunit content of Golgi-cell-to-granule-cell synapses in alpha 6-/- animals remained unaltered, as did the frequency of alpha 1 immunopositive synapses in the glomeruli. Furthermore, no change was apparent in the expression of the alpha 1, beta 2 and gamma 2 subunits in Purkinje cells and interneurons of the molecular layer. These results demonstrate that in alpha 6-/- mice, the cerebellum expresses only half of the number of GABA(A) receptors present in wild-type animals. Since these animals have no gross motor deficits, synaptic integration in granule cells is apparently maintained by alpha 1-subunit-containing receptors with an altered overall subunit composition, and/or by changes in the expression of other ligand and voltage gated channels.