Drug-drug interaction (DDI) is referred as the changes of physical and chemical properties, as well as the pharmacokinetics or pharmacodynamics of drugs administered simultaneously or consecutively. The clinical results for drug-drug interaction could be divided into good clinical efficacy and adverse interaction. With the kinds of drugs increasing every year, new drug resistances spring up frequently. This phenomenon makes drug combination increased so that the drug interaction, especially the adverse interaction emerged. The mechanisms of in vivo drug-drug interaction are relevant to a number of factors, including drug-metabolizing enzyme systems and membrane transporters. Recent studies have revealed the important role played by transporters in drug absorption, distribution, metabolism and elimination. In order to avoid severe side effects mediated by transporters and to promote rational combination in clinics, the mechanisms of intestinal absorption and renal excretion mediated by transporters are reviewed.