All segments of the gastrointestinal tract are comprised of an elaborately folded epithelium that expresses a variety of cell types and performs multiple secretory and absorptive functions. While the apical membrane expresses the electrolyte transporters that secrete or absorb electrolytes and water, basolateral transporters regulate the secretory or absorptive rates. During gastric acid formation, Cl-/HCO3- and Na+/H+ exchange and other transporters secure Cl- re-supply as well as pH and volume regulation. Gastric surface cells utilize ion transporters to secrete HCO3-, maintain pHi during a luminal acid load and repair damaged surface areas during the process of epithelial restitution. Na+/H+ exchange and Na+/HCO3- cotransport serve basolateral acid/base import for gastroduodenal HCO3- secretion. The gastric and duodenal epithelium also absorbs salt and water. Recent molecular information on novel ion transporters expressed in the gastric and duodenal epithelium has exploded; however, a function has not been found yet for all transporters. The purpose of this review is to summarize current knowledge on the molecular identity and cellular function of basolateral ion transporters in the gastric and duodenal epithelium. © 2010 The Authors. Journal compilation © 2010 Scandinavian Physiological Society.