Flavin-containing monooxygenases (FMOs) play significant roles in the metabolism of drugs and endogenous or foreign compounds. In this study, the regional distribution of FMO isoforms 1, 3, and 4 was investigated in male Sprague-Dawley rat liver and kidney using immunohistochemistry (IHC). Rabbit polyclonal antibodies to rat FMO1 and FMO4, developed using anti-peptide technology, and commercial anti-human FMO3 antibody were used; specificities of the antibodies were verified using Western blotting, immunoprecipitation, and IHC. In liver, the highest immunoreactivity for FMO1 and FMO3 was detected in the perivenous region, and immunoreactivity decreased in intensity toward the periportal region. In contrast, FMO4 immunoreactivity was detected with the opposite lobular distribution. In the kidney, the highest immunoreactivity for FMO1, -3, and -4 was detected in the distal tubules. FMO1 and FMO4 immunoreactivity was also detected in the proximal tubules with strong staining in the brush borders, whereas less FMO3 immunoreactivity was detected in the proximal tubules. Immunoreactivity for FMO3 and FMO4 was detected in the collecting tubules in the renal medulla and the glomerulus, whereas little FMO1 immunoreactivity was detected in these regions. The FMO1 antibody did not react with human liver or kidney microsomes. However, the FMO4 antibody reacted with male and female mouse and human tissues. These data provided a compelling visual demonstration of the isoform-specific localization patterns of FMO1, -3, and -4 in the rat liver and kidney and the first evidence for expression of FMO4 at the protein level in mouse and human liver and kidney microsomes.Flavin-containing monooxygenases (FMOs) are microsomal enzymes that catalyze oxidation of pharmaceutical drugs, pesticides, and endogenous compounds. In general, FMO oxidation increases the polarity of substrates, aiding in excretion and detoxification; however, some substrates are bioactivated to reactive or toxic metabolites. Five expressed FMO isoforms (FMO1-5) have been detected in humans . FMO isoforms have different substrate selectivity and exhibit distinct sex-, tissue-, age-, and speciesdependent expression profiles .The liver typically contains the largest concentrations of xenobiotic-metabolizing enzymes. Adult human liver mRNA exhibits high FMO3 expression, moderate FMO4 expression, and extremely low FMO1 expression (Dolphin et al., 1996;Cashman and Zhang, 2006). In contrast, rat or mouse liver has moderate FMO1 protein expression (Falls et al., 1995;Lattard et al., 2002). To our knowledge, FMO localization in liver has been elucidated only in mice by in situ hybridization (Janmohamed et al., 2004). FMO1 and FMO5 mRNAs were detected across the acinus, with a concentration gradient decreasing from the perivenous (PV) to the periportal (PP) hepatocytes. FMO2, -3, and -4 mRNAs were localized heavily in the PP region (Janmohamed et al., 2004). The heterogeneous expression patterns of FMO isoforms within the liver may suggest distinct roles in metabol...