Flavin-containing monooxygenase (FMO) catalyses the oxygenation of numerous heteroatom-containing drugs, chemicals and agricultural agents; its physiological role is unknown. The term FMO covers a number of flavoproteins: the nomenclature system is outlined. The FMO genes are localised on human chromosome 1q. The three-dimensional structure has not been determined but other physical characteristics of the protein are described, as are genetic polymorphisms that affect FMO enzymatic activity. The biochemical properties of FMO are discussed in detail to put the monooxygenase system in perspective with other systems. The catalytic mechanism is best known for the pig FMO1, as illustrated here. This enzyme is also used as the basis for structure-function studies, but the most important FMO in human drug and xenobiotic metabolism is probably FMO3 and studies of its substrate specificity and stereochemical considerations are described. Finally, the role of FMO in toxicological aspects are discussed.