Intestinal absorption and renal secretion of ionic drugs are controlled by a number of drug transporters expressed at the brush-border and basolateral membranes of epithelial cells. Over the last several years, considerable progress has been made regarding the molecular identification and functional characterization of drug transporters. Under some physiological and pathophysiological conditions, the expression and transport activity of drug transporters are changed, affecting the pharmacokinetics of substrate drugs. The regulation of transport activity in response to endogenous and exogenous signals can occur at various levels such as transcription, mRNA stability, translation, and posttranslational modification. Transcriptional regulation is of particular interest, because changes in transport activity are dynamically regulated by increases or decreases in levels of mRNA expression. The tissue-specific expression of drug transporters is also under transcriptional control, and recent studies using clinical samples from human tissues have revealed the expression profiles of drug transporters in the human body. The purpose of this research updates is to review the recent progress in the study of the gene expression and regulation of intestinal and renal drug transporters.