The accumulating evidence has revealed that drug transporters have essential roles in the delivery and excretory processes of drugs and their metabolites. Inhibition or induction of drug transporters can affect pharmacokinetic properties and therapeutic efficacy of a drug. Thus, the characterization of drug-transporter interactions becomes important for the selection of compounds to avoid transporter associated absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) issues. Additionally, the potential use of absorptive transporters for drug delivery has been recognized for drug design. In vitro and in vivo approaches have been developed for studying the transporter activities. In vitro assays can rapidly provide the information for identifying interaction of a compound and a particular transporter and have proved to be amenable to high throughput approaches. Therefore, the studies are conducted in early drug discovery. In this article, in vitro methods are reviewed, including cell free and cell-based assays. Their applications, limitations and impact on drug discovery are discussed.