Many drug–drug interactions (
DDI
s) are based on alterations of the plasma concentrations of a victim drug due to another drug causing inhibition and/or induction of the metabolism or transporter‐mediated disposition of the victim drug. In the worst case, such interactions cause more than tenfold increases or decreases in victim drug exposure, with potentially life‐threatening consequences. There has been tremendous progress in the predictability and modeling of
DDI
s. Accordingly, the combination of modeling approaches and clinical studies is the current mainstay in evaluation of the pharmacokinetic
DDI
risks of drugs. In this paper, we focus on the methodology of clinical studies on
DDI
s involving drug metabolism or transport. We specifically present considerations related to general
DDI
study designs, recommended enzyme and transporter index substrates and inhibitors, pharmacogenetic perspectives, index drug cocktails, endogenous substrates, limited sampling strategies, physiologically‐based pharmacokinetic modeling, complex
DDI
s, methodological pitfalls, and interpretation of
DDI
information.