Absorption and secretion of ions in gastrointestinal and other epithelial tissues require the concerted activities of ion pumps, channels, symporters, and exchangers, which operate in coupled systems to mediate transepithelial transport. Our understanding of the identities, membrane locations, and biochemical activities of epithelial ion transporters has advanced significantly in recent years, but major gaps and uncertainties remain in our understanding of their physiological functions. Increasingly, this problem is being addressed by the analysis of mutant mouse models developed by gene targeting. In this review, we discuss gene knockout studies of the secretory isoform of the Na(+)-K(+)-2Cl(-) cotransporter, isoforms 1, 2, and 3 of the Na(+)/H(+) exchanger, and the colonic H(+)-K(+)-ATPase. This approach is leading to a clearer understanding of the functions of these transporters in the living animal.