The discovery of unidirectional, ATP-dependent canalicular transport systems (also termed "export pumps") for bile salts, amphiphilic anionic conjugates, lipophilic cations, and phospholipids has opened new opportunities for understanding biliary physiology and the pathophysiology of cholestasis. In addition, ATP-independent canalicular transport systems for glutathione and bicarbonate contribute to (bile acid-independent) bile formation. Canalicular excretion of bile salts and several non-bile acid organic anions is impaired in various experimental models of cholestasis. Recent cloning of several canalicular transport systems now facilitates studies on their molecular regulation in cholestasis. Although the picture is far from complete, experimental evidence now exists that decreased or even absent expression of canalicular transport proteins may explain impaired transport function resulting in hyperbilirubinemia and cholestasis. With the increasing availability of molecular probes for these transport systems in humans, new information on the molecular regulation of canalicular transport proteins in human cholestatic liver diseases is beginning to emerge and should bring new insights into their pathophysiology and treatment. This article gives an overview on molecular alterations of canalicular transport systems in experimental models of cholestasis and discusses the potential implications of these changes for the pathophysiology of cholestasis.