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Many drugs are the subject of multipathway oxidative metabolism catalyzed by one or more cytochromes P450 or flavin-containing monooxygenases (FMOs). This complicates assessment of the role of individual enzymes in metabolizing the drug and, hence, in understanding its pharmacogenetics. To define the role of FMOs in drug metabolism, we produced FMO-deficient mice.An Fmo1(−/−), Fmo2(−/−), Fmo4(−/−) mouse line was produced by using chromosomal engineering and Cre-loxP technology. To assess the utility of the mutant mouse line, it was used to investigate the role of FMO in the metabolism of and response to the antidepressant imipramine, which has four major metabolites, three produced by cytochromes P450 and one, imipramine N-oxide, solely by FMO1.On treatment with imipramine, wild-type mice became sedated and produced imipramine N-oxide in the brain and other tissues. In contrast, knockout mice did not produce imipramine N-oxide, but showed exaggerated pharmacological behavioural responses, such as tremor and body spasm, and had a higher concentration of the parent compound imipramine in the serum and kidney and there was an increase in desipramine in the brain.The absence of FMO1-mediated N-oxidation of imipramine results in enhanced central nervous system effects of the drug. The results provide insights into the metabolism of imipramine in the brain and may explain the basis of the adverse reactions to the drug seen in some patients. The knockout mouse line will provide a valuable resource for defining the role of FMO1 in the metabolism of drugs and other foreign chemicals.