It is now widely accepted that proton secretion by the collecting duct is mediated, in part, by an H(+)-K(+)-adenosinetriphosphatase (H(+)-K(+)-ATPase). Controversy persists regarding which H(+)-K(+)-ATPase isoform is expressed in kidney. Several laboratories have reported preliminarily the amplification from kidney of stomach and/or colon-identical products using gastric or colonic-specific primers in the polymerase chain reaction (PCR). We have developed highly specific probes for the catalytic subunit using reverse transcriptase-PCR with gastric- or colonic-specific primers. The resulting cDNAs were verified by sequencing and were then used in Northern analysis of whole kidney total RNA obtained from one of the following three groups of rats: 1) controls, 2) chronic hypokalemia, or 3) chronic metabolic acidosis. Probes for both the colonic and gastric alpha-subunit H(+)-K(+)-ATPase isoforms hybridized to whole kidney total RNA derived from potassium-replete control rats. A marked elevation of colonic mRNA abundance, but not gastric message, was observed in response to chronic hypokalemia induced by dietary potassium deprivation. Elevation of either gastric or colonic mRNA was not observed with chronic metabolic acidosis. Under the conditions of the present study, it appears that the mRNA encoding the colonic alpha-isoform of the H(+)-K(+)-ATPase in kidney is upregulated by chronic hypokalemia but not by chronic metabolic acidosis. The observation that the gastric H(+)-K(+)-ATPase alpha-isoform does not appear to be regulated in either condition suggests that this isoform is expressed constitutively in kidney.