The efficacy and safety of pharmacotherapies are determined by the complex processes involved in the interactions between drugs with the human body, including pharmacokinetic aspects. Among pharmacokinetic factors, it has been recognized that drug transporters play critical roles for absorption, distribution and excretion of drugs, regulating the membrane transport of drugs. The vast amounts of information on drug transporters collected in the past 20 years have been organized according to biochemical, molecular, genetic, and clinical analyses. Novel technologies, public databases, and regulatory guidelines have advanced the use of such information in drug development and clinical practice. In this review, we selected some clinically important drug transporters expressed in the intestine and liver, and introduced the research history and current knowledge of their pharmacokinetic, pathophysiological, and pharmacogenetic implications.