Drug transporters act as determinant for the clearance of drugs from the blood circulation in the liver and kidney. Inhibition of such transporters by drugs causes accumulation of their substrate drugs, and thereby increasing the risk of adverse reactions in combination use. In drug development, it is prerequisite to assess the inhibition potency of the investigation drugs against major drug transporters. Recently, endogenous biomarkers have emerged to advance this risk assessment in the clinical stage. We identified some endogenous substrates in healthy volunteers using well characterized inhibitors and metabolomic approach for the drug transporters such as OATP1B1/1B3, OAT1, OAT3 and OCT2, MATE1/2-K whose pharmacokinetic parameters, such as AUC and renal clearance (CLR), changed according to the degree of inhibition of drug transporters. Physiologically based pharmacokinetic (PBPK) models for the endogenous substrates have been also constructed to explain the effect of inhibitors. PBPK-model based approach are highly expected to extrapolate the biomarker data to the DDI. The endogenous biomarkers are highly expected to improve predictability of the DDI in early phase of clinical stage of drug development, and aids design of the strategy to de-risk of the DDI in the clinical settings.