Nitric oxide (NO) modifies the functions of a variety of proteins containing cysteine thiols or transition-metal centers, particularly by S-nitrosylation. In inflamed liver, NO is overproduced and hepatic drug-metabolizing enzymes, the flavin-containing monooxygenases (FMOs) and cytochrome P450s (CYPs), are suppressed. However, the NO-related mechanisms underlying the loss of these activities are not well understood, particularly for FMOs. In this study, we suggest that FMO3, the major FMO in human liver, is modified post-translationally by NO. This hypothesis is based on the imbalance observed between the decrease in FMO3 expression (40.7% of controls) and FMO3-specific ranitidine N-oxidation activity (15.1%), and on the partial or complete reversibility of FMO inhibition by sulfhydryl-reducing regents such as DTT (effective on both S-S and S-NO adducts) and ascorbate (effective on S-NO only). Furthermore, NO donors (SNP, SNAP, and Sin-1), including the pure NO donor DEA/NO, directly suppressed in vitro FMO activity (N- or S-oxidation of ranitidine, trimethylamine, and thiobenzamide) in human liver microsomal proteins and recombinant human FMO3. These activities were restored completely after treatment with DTT or ascorbate. These results suggest that NO-mediated S-nitrosylation is involved in the rigorous inhibition of FMO activity in vitro and in vivo, resulting in the suppression of FMO-based drug metabolism or detoxification.