The alpha subunit complements of natural gamma-aminobutyric acidA (GABAA) receptor subpopulations were investigated by their purification from mammalian cerebral cortex and cerebellum by immunoaffinity chromatography using antibodies raised against peptide sequences unique to the alpha 1, alpha 2, alpha 3, and alpha 6 subunits. Receptors purified from cerebral cortex by anti-Cys alpha 2 414-424 and anti-Cys alpha 3 454-467 antibody affinity columns in series had immunoreactivity with alpha 2 and alpha 3 but not alpha 1 subunit-specific antibodies. Receptors purified from cerebellum by a new affinity column matrix, anti-alpha 6 1-16 Cys whole antibody, or the Fab fragment thereof, enriched for alpha 6 subunit immunoreactivity. A further series of experiments demonstrated the partial coexistence of this alpha 6 subunit immunoreactivity with that for the alpha 1 but not the alpha 2 and alpha 3 subunits. These results provide additional evidence for the existence of GABAA receptor subpopulations with heterogeneous alpha subunit complements yielding increased structural diversity of natural GABAA receptors. Furthermore, they substantiate previous findings implicating the presence of two alpha subunits per receptor oligomer.