The gamma-aminobutyric acid(A)/benzodiazepine receptor complexes from bovine cerebral cortex were purified by immunoaffinity chromatography, and the main component peptide subunits were characterized. The peptide band originally thought to be a single beta-subunit [57,000 M(r) band in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)] is composed of at least four different peptides of 54,000-57,000 M(r). Two peptides of 55,000 and 57,000 M(r) were recognized by the beta-subunit-specific monoclonal antibody 62-3Gl. Peptides in the range of 54,000-57,000 M(r) were photoaffinity-labeled with [H-3]muscimol. A different 57,000 M(r) peptide was photoaffinity-labeled by [H-3]flunitrazepam, but neither was recognized by the monoclonal antibody 62-3Gl nor photoaffinity-labeled with [H-3]muscimol. Some peptides could be identified by their differential mobility shift in SDS-PAGE after treatment with endoglycosidase H. Two additional subunit peptides of 51,000 and 53,000 M(r) were also photoaffinity-labeled by [H-3]flunitrazepam and reacted with antiserum A. However, the 57,000 M(r) peptide that also was photoaffinity-labeled by [H-3]flunitrazepam did not react with antiserum A.