Our laboratory recently isolated and sequenced cDNAs encoding the microsomal flavin-containing monooxygenases (FMOs) from rabbit liver and rabbit lung. As a first step in understanding the molecular bases for the catalytic and physical differences between these enzymes, we have expressed them in COS-1 cells and compared the properties of the recombinant and native microsomal proteins. Microsomes from transfected cells were examined immunochemically by immunoblotting and catalytically by following methimazole oxidation in the presence and absence of various modulators. The expressed and native FMOs have the same mobilities in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the same responses to pH, sodium cholate, magnesium, and temperature, all of which serve to differentiate between the lung and liver enzymes. Analysis of methimazole metabolism in microsomes isolated from rabbit liver or lung showed biphasic kinetics, indicative of two or more enzymes taking part in the reaction. In contrast, the kinetics of methimazole oxidation catalyzed by the expressed FMOs were clearly linear and matched one of the phases observed with the native preparations. Chlorpromazine and imipramine, which are not substrates for the pulmonary FMO, were found to be competitive inhibitors of the high affinity reaction in pulmonary microsomes. These results, and others, indicate that both rabbit lung and liver contain more than one form of FMO.