Acidified extracts of rat antral stomach chromatographed on octadecylsilane cartridges contained material that inhibited the binding of [3H]Ro 5-4864 (4'-chlorodiazepam) and [3H]nitrenidipine to "peripheral-type" benzodiazepine receptors and dihydropyridine Ca2+-channel antagonist binding sites respectively. This material reduced the apparent affinities of both radioligands without significantly affecting the maximum number of binding sites. In contrast, the binding of [3H]diazepam, [3H]Ro 15-1788 (ethyl-8-fluoro-5,6-dihydro-5-methyl-6-oxo-4H-imidazo [1,5a][1,4] benzodiazepine-3-carboxylate), and [3H]3-carbomethoxy-beta-carboline to "brain-type" benzodiazepine receptors and [3H]dihydroalprenolol binding to beta-adrenergic receptors were unaffected by this material. Subsequent column chromatography on hydroxylapatite purified this material by greater than 2000-fold. This semi-purified substance was resolved by reverse phase HPLC as one u.v. adsorbing peak that inhibited both [3H]Ro 5-4864 and [3H]nitrendipine binding. The activity of this 16,000 dalton substance was destroyed completely by both heat treatment and pronase and partially reduced by trypsin. Furthermore, the inhibitory activity of this substance was enhanced by Ca2+ in a concentration-dependent fashion (0.1 to 10 mM). Comparison of TLC scans of 2-9,10[3H]dipalmitoyl-phosphatidylcholine incubated with either the HPLC purified material or authentic phospholipase A2(PLA2) (Naja naja) revealed that this substance has enzymatic properties indistinguishable from PLA2. These findings suggest that this endogenous protein may be a PLA2 isoenzyme which may modify both "peripheral-type" benzodiazepine receptors and dihydropyridine Ca2+-channel antagonist binding sites.