Renal transporters play a critical role in the renal secretion of prescription drugs and endogenous metabolites. Inhibition of these transporters can increase the plasma exposure of a co-administered drug by reducing its renal clearance, potentially resulting in clinically significant drug-drug interactions (DDIs). The ICH M12 guideline promotes the use of endogenous substrates as biomarkers offers a promising approach for assessing transporter inhibition during early-phase clinical studies, potentially reducing reliance on traditional probe-based DDI trials. This strategy may reduce or eliminate the need for dedicated DDI studies using exogenous probe substrates, thereby streamlining drug development and advancing precision medicine. This review provides an overview of the discovery, evaluation, and application of renal transporter biomarkers-specifically endogenous metabolites-in the context of transporter-mediated DDI risk assessment. We highlight the use of in vitro and in vivo models, including transporter-overexpressing cell systems, knockout mice, and clinical DDI samples, to identify and validate biomarkers for renal transporters. Human genetic studies further support biomarker discovery by linking transporter variants to metabolite levels. Analytical tools like targeted and untargeted metabolomic approaches are essential for biomarker identification and quantification. Additionally, physiologically based pharmacokinetic (PBPK) modeling is discussed as a critical tool for translating biomarker data into clinical DDI predictions.