The flavin‐containing monooxygenase (FMO) is a drug‐metabolizing enzyme that oxygenates sulfur‐, nitrogen‐, phosphorous‐ and selenium‐containing compounds. Amines and sulfides are very prevalent in drugs and drug candidates, and FMO could play an important role in drug discovery. Generally, FMO‐mediated metabolism converts compounds to more polar, readily excreted metabolites, and this constitutes a detoxication process. However, sometimes, FMO produces electrophilic metabolites that inhibit other enzyme systems because FMO is quite recalcitrant to inhibition. Because FMO is not readily inhibited or induced, most of its functional variability is not due to environmental factors but due to genetic polymorphisms. Compared with cytochrome P450, drugs and drug candidates that are metabolized by FMO possess less potential for toxicity and adverse drug–drug interactions. Nucleophilic drugs and drug candidates are oxygenated by FMO, and some of these oxygenated metabolites can be readily retroreduced to the parent compound quite efficiently. One class of highly nucleophilic agent that is not oxygenated by FMO includes endogenous physiological nucleophiles such as glutathione or cysteine. The lack of S‐oxygenation of these physiological nucleophiles probably spares the cell from unnecessary consumption of NADPH reductive equivalents as well as from the loss of thiaphile cytoprotective agents such as glutathione. With regard to drug or drug candidate metabolism, introducing a functional group into drug candidates that are metabolized by FMO may be beneficial in drug development and might distribute the metabolism of the drug candidate over a wider set of enzymes as well as potentially provide FMO metabolites that are generally polar, nontoxic, and readily excreted. By avoiding metabolism (and bioactivation) by cytochrome P450, the prospects for increasing druglike properties and decreasing adverse drug–drug interactions of a drug candidate are likely increased. Distributing the metabolism of drugs over a wide range of metabolic processes including FMO might decrease reliance on one metabolic pathway and decrease toxicity and adverse drug–drug interactions.