Abstract The use of stable isotopes in drug metabolism studies and drug design are described here. Stable isotopes have been reported as tracers and labels, which allow scientists to utilize a variety of experimental techniques to monitor and study drug metabolism without the use of radioisotopes. In addition, recent findings relating to incorporation of deuterium as a strategy for drug design is described as well. Guidance and mechanistic reasoning for deuterated drugs as tools and clinical compounds to solve metabolism-related issues are provided. This includes, but is not limited to, half-life, bioavailability, reactive metabolite formation, and drug-drug interactions. Clinical case studies are included, with guidance on how to effectively capitalize on the chemical advantages of deuterium for metabolism-guided design.