Two classes of H pumps, H-K-ATPase and H-ATPase, contribute to luminal acidification and HCO(3) transport in the collecting duct (CD). At least two H-K-ATPase alpha-subunits are expressed in the CD: HKalpha(1) and HKalpha(2). Both exhibit K dependence but have different inhibitor sensitivities. The HKalpha(1) H-K-ATPase is Sch-28080 sensitive, whereas the pharmacological profile of the HKalpha(2) H-K-ATPase is not completely understood. The present study used a nonpharmacological, genetic approach to determine the contribution of HKalpha(1) and HKalpha(2) to cortical CD (CCD) intercalated cell (IC) proton transport in mice fed a normal diet. Intracellular pH (pH(i)) recovery was determined in ICs using in vitro microperfusion of CCD after an acute intracellular acid load in wild-type mice and mice of the same strain lacking expression of HKalpha(1), HKalpha(2), or both H-K-ATPases (HKalpha(1,2)). A-type and B-type ICs were differentiated by luminal loading with BCECF-AM and peritubular chloride removal from CO(2)/HCO(3)-buffered solutions to identify the membrane locations of Cl/HCO(3) exchange activity. H-ATPase- and Na/H exchange-mediated H transport were inhibited with bafilomycin A(1) (100 nM) and EIPA (10 microM), respectively. Here, we report 1) initial pH(i) and buffering capacity were not significantly altered in the ICs of HKalpha-deficient mice, 2) either HKalpha(1) or HKalpha(2) deficiency resulted in slower acid extrusion, and 3) A-type ICs from HKalpha(1,2)-deficient mice had significantly slower acid extrusion compared with A-type ICs from HKalpha(1)-deficient mice alone. These studies are the first nonpharmacological demonstration that both HKalpha(1) and HKalpha(2) contribute to H secretion in both A-type and B-type ICs in animals fed a normal diet.