The kinetics and pharmacology of the isoquinoline and benzodiazepine binding sites of the omega3 or peripheral-type benzodiazepine receptors were studied using the specific ligands [3H] 7-chloro-5-(4-chlorophenyl)-1,3-dihydro-1-methyl-2H-1,4-benzodiazepin -2-one ([3H]PK11195) and [3H]1-(2-Chlorophenyl)-N-methyl-N-(1-methylpropyl)-3-isoquinolinecarb oxamide ([3H]RO5-4864), respectively. Binding of both ligands was saturable, reversible, displayed nanomolar affinity, and best fit to a single site model. Occipital cortex and cerebellum displayed highest and lowest densities of binding sites respectively; for both ligands. Bmax values of [3H]PK11195 were several-fold higher than that of [3H]RO5-4864 in all regions studied consistent with their binding to distinct subunits of the human peripheral-type benzodiazepine receptor heteromeric complex. However, the isoquinoline and benzodiazepine ligands were found to be mutually competitive at nanomolar concentrations suggesting allosteric interactions between these two sites. Competition binding experiments showed that the binding of both ligands was displaced by diazepam with Ki values in the nM range, and by clonazepam in the microM range. The novel peripheral-type benzodiazepine receptor ligand 2-(4-fluorophenyl)-N,N-di-n-hexyl-1H-indole-3-acetamide (FGIN1-27) displaced only [3H]PK11195 binding with high potency. Heterogeneity of the two sites is observed, manifested by their differential susceptibility towards detergents and alcohols. Histidine residue modification by diethylpyrocarbonate treatment abolished only [3H]PK11195 binding but had no effect on [3H]RO5-4864 binding. These studies demonstrate that the isoquinoline and benzodiazepine sites on the peripheral-type benzodiazepine receptor in human brain manifest many pharmacological characteristics that are distinct from each other and from rodent brain peripheral-type benzodiazepine receptors.