In cerebellum, GABAA receptors containing alpha6 subunits are expressed exclusively in granule cells. The number of alpha6 receptor subtypes formed in these cells and their subunit composition presently are not known. Immunoaffinity chromatography on alpha6 subunit-specific antibodies indicated that 45% of GABAA receptors in cerebellar extracts contained alpha6 subunits. Western blot analysis demonstrated that alpha1, beta1, beta2, beta3, gamma2, and delta subunits co-purified with alpha6 subunits, suggesting the existence of multiple alpha6 receptor subtypes. These subtypes were identified using a new method based on the one-by-one immunochromatographic elimination of receptors containing the co-purifying subunits in parallel or subsequent experiments. By quantification and Western blot analysis of alpha6 receptors remaining in the extract, the proportion of alpha6 receptors containing the eliminated subunit could be calculated and the subunit composition of the remaining receptors could be determined. Results obtained indicated that alpha6 receptors in cerebellum are composed predominantly of alpha6betaxgamma2 (32%), alpha1alpha6betaxgamma2 (37%), alpha6betaxdelta (14%), or alpha1alpha6betaxdelta (15%) subunits. Other experiments indicated that 10%, 51%, or 21% of alpha6 receptors contained homogeneous beta1, beta2, or beta3 subunits, respectively, whereas two different beta subunits were present in 18% of all alpha6 receptors. The method presented can be used to resolve the total number, subunit composition, and abundancy of GABAA receptor subtypes in the brain and can also be applied to the investigation of other hetero-oligomeric receptors.