The solubilization and partial purification from rat brain cortex homogenates of [3H]gamma-aminobutyric acid (GABA) and [3H]diazepam recognition sites and of their endogenous modulators (GABA-modulin and an endogenous compound which specifically bound [3H]diazepam) are reported. A high percentage of GABA binding sites (virtually free of benzodiazepine binding sites) was solubilized from homogenates of rat brain cortex incubated at 0 degree C with 1% Triton X-100 and a mixture of protease inhibitors. A large proportion of benzodiazepine binding sites was solubilized in the absence of apparent GABA binding capacity by incubating crude synaptic membrane preparations at 37 degree C with 0.05% Triton X-100. The characteristics of these two solubilized binding sites resemble those of the membrane-bound binding sites. However, unlike the membrane-bound sites, solubilized GABA and benzodiazepine binding sites are insensitive to GABA stimulation, while solubilized GABA binding sites are no longer protected by the benzodiazepines against heat inactivation. These results indicate that GABA and benzodiazepine recognition sites reside in two different molecules which, when bound to membranes, can interact reciprocally and modulate their binding affinity for specific ligands.