This paper reviews scientific contributions on the identification and/or quantification of metabolites of drugs of abuse in in vitro assays or various body samples using hyphenated mass spectrometry. Gas chromatography-mass spectrometry (GC-MS) as well as liquid chromatography-mass spectrometry (LC-MS) approaches are considered and discussed if they have been reported in the last five years and are relevant to clinical and forensic toxicology or doping control. Workup and artifact formation are discussed, and typical examples of studies of the metabolism of designer drugs, doping agents, herbal drugs, and synthetic cannabinoids are provided. Procedures for quantifying metabolites in body samples for pharmacokinetic studies or in enzyme incubations for enzyme kinetic studies are also reviewed. In conclusion, the reviewed papers showed that both GC-MS and LC-MS still have important roles to play in research into the metabolism of drugs of abuse, including doping agents.