The Flavin-containing monooxygenase (FMO) system is used for oxidation reactions in drug metabolism. The major difference between this system and the Cytochrome P450 monooxygenase system is that the FMO system does not act to oxidize carbon atoms. Also in contrast to P450, the FMO system is not induced by exposure to drugs or environmental pollutants .

Otherwise, the FMO system is similar to the cytrochrome P450 system in that both require NADPH and oxygen; multiple isozymes are known for both; and they are both localized in microsomes of the endoplasmic reticulum.