Gastric glands, isolated from rabbit, were permeabilized with digitonin to permit measurement of H+-K+-adenosinetriphosphatase (ATPase) activity and proton transport in situ. Measurement of proton gradient formation using acridine orange fluorescence showed two phases of ATP-driven proton accumulation; one phase occurs spontaneously in KCl medium and one phase requires the K+ ionophore valinomycin. Valinomycin was found to increase H+-K+-ATPase activity, indicating that the second phase is because of increased proton transport rather than a decrease in proton leak rate. The acid-activated, irreversible inhibitor, omeprazole, was used to selectively eliminate the H+-K+-ATPase molecules associated with the spontaneous component of proton transport. After omeprazole treatment a residual, valinomycin-dependent component of proton transport could be demonstrated. These results are interpreted as evidence for two compartments of H+-K+-ATPase, separated by a barrier that prevents K+ diffusion and pH equilibration. The two compartments may be separated also on the basis of anion selectivity. The spontaneously active compartment was found to be functional with various anions, including sulfate and isethionate, whereas the valinomycin-dependent component is highly selective for chloride. The proportion of H+-K+-ATPase that exists in each compartment was quantitated by measuring the fraction of total ATPase activity that could be inhibited by omeprazole in the absence and presence of valinomycin. For glands that were preconditioned with cimetidine, approximately 30% of the inhibitable enzyme was found associated with the spontaneous compartment, and this fraction increased to approximately 70% with histamine preconditioning.(ABSTRACT TRUNCATED AT 250 WORDS)