In the gastrointestinal tract potassium channels energize transport of salt and solutes across epithelial cells. Additionally, they play an important role for the stabilization of the cell volume, and they are needed for normal cell proliferation, differentiation, and apoptosis. In this study we investigated the expression of potassium channel genes along the mouse gastrointestinal tract by real-time PCR. In contrast to other studies using the complete intestinal wall, only mucosal cells were used for the preparation of mRNA. Based on the literature and EST data, 24 genes have been pre-selected as likely candidates for epithelial potassium channels. In gastric mucosa, highest expression levels were observed for KCNQ1, KCNE2, KCNE1, and two members of the KCNJ family. In the mucosal cells of duodenum, jejunum, and ileum KCNK5, KCNQ1, and KCNN4 showed strongest levels of expression. In colonic epithelial cells, KCNN4, KCNE3, KCNQ1, KCNH2, KCNH8, KCNMA1, KCNK6, KCNK1, and KCNK5 were highly expressed. Among those channels, KCNK5 showed a distinct expression along the colonic crypt axis with absence of expression at the crypt base and strong expression in the upper part of the crypt and in surface cells. In conclusion, these data provide helpful information for studies focussing on epithelial cell function in the gastrointestinal tract.