Hepatic flavin-containing monooxygenase (FMO) activity of microsomes from adult CD-1, Swiss-Webster, C57BL/6, and DBA/2 mice was found to be significantly higher in females than in males. Based on protein and mRNA levels in CD-1 mice, FMO forms responsible for the gender difference in FMO activity were FMO1 and FMO3. FMO1 expression was two to three times higher in female mice compared with males; FMO3, however, which was expressed at levels equivalent to FMO1 in female mice, was not detected in males. The expression of FMO5 was approximately equal in both sexes. FMO2 and FMO4 transcripts were not evident in hepatic mRNA from mice. Protein and mRNA levels appear to be coregulated with regard to gender-selective or gender-specific expression of FMO1 or FMO3, respectively. FMO5, which demonstrates no gender-selective expression in mice, may be regulated by different mechanisms. Examination of protein levels among Swiss-Webster, C57BL/6, and DBA/2 strains revealed a gender-dependent expression of FMO isozymes identical to the CD-1 strain.