Cholestasis may result from genetic or acquired defects in bile secretion. Cloning of hepatobiliary transporter genes has advanced our understanding of the molecular basis of bile formation and cholestasis. Hereditary mutations of transporter genes, exposure to cholestatic injury (eg, drugs, hormones, cytokines), or the combination of both can result in reduced expression and function of hepatobiliary transport systems. These molecular changes impair hepatic uptake and excretion of bile salts and other organic anions (eg, bilirubin). Other molecular changes contibuting to cholestasis include alterations of membrane fluidity, cytoskeleton, vesicle movement, and cell contacts. Transporter mutations can be diagnosed at the molecular genetic level. Gene therapy and hepatocyte transplantation could be used in the future to correct hereditary transport defects. Drugs used to treat cholestatic liver diseases (eg, ursodeoxycholic acid) stimulate and partially restore defective transporter expression and function. New information on the molecular mechanisms of cholestasis should lead to the development of novel drugs for cholestatic liver diseases.