The expression of the three alpha-isoforms of Na(+)-K(+)-adenosine triphosphatase (ATPase) was examined in rat brain and rat kidney by Northern blot analysis. All three isoforms were detected in brain tissue while alpha 1-isoform was observed in whole kidney, suggesting that either this isoform was solely expressed in this organ or that alpha 2- and/or alpha 3-isoforms were not detected only because of their restricted distribution among a minority of specialized tubular cells. To distinguish between these two possibilities, in situ hybridization with rat alpha 1-, alpha 2-, and alpha 3-ATPase cRNA was performed on rat kidney sections. Results show that alpha 1-isoform expression largely predominates in the loop of Henle, distal tubule, and cortical collecting tubule. The labeling was drastically reduced by preincubation of sections with RNase. A sense cRNA probe, used as control, did not hybridize. With alpha 2- and alpha 3-probes, the labeling was low and uniformly distributed. In contrast, these two isoforms were clearly expressed in the brain, together with alpha 1. We conclude that only alpha 1-isoform of the Na(+)-K(+)-ATPase is detectable along the rat nephron. Its expression predominates in the tubular segments known to have a high Na(+)-K(+)-ATPase activity.