The role of the intestine in systemic acid-base regulation is not well known. Here, we investigated the distribution of 14 acid- base transporter genes from three families: Slc9 (Na/H- exchanger), Slc4 and Slc26 (anion exchangers) along the murine stomach, small and large intestine. mRNA for the Na/H exchanger isoforms NHE1, NHE2, NHE3, and NHE8 was found in all segments. In contrast, the expression of the Slc4 and Slc26 members showed distinct patterns. Slc26a3 was mostly expressed in distal colon, whereas Slc26a7 and Slc26a9 in stomach. The "kidney"-isoform (Slc4a-A) of the electrogenic Na-bicarbonate cotransporter was only found in ileum and colon, whereas the "pancreatic" isoform Slc4a-B along the whole intestine. The electroneutral Slc4a7 was mainly expressed in duodenum and jejunum. Slc4a9 could not be detected in the intestine despite earlier reports. Thus, there is a distinct spatial arrangement of intestinal acid-base transporters that may contribute to the segment-specific intestinal functions. The regulation of these genes during acid-base disturbances is further studied.