We are developing a flavin-containing (Fmo) knock-out mouse for Fmo2 that will be utilized to elucidate the role of active human FMO isoform 2 (FMO2.1) in xenobiotic metabolism and toxicity. Since FMO2 is primarily expressed in lung this will provide information on how 27% of African-Americans and 5% of Hispanics that carry the FMO2*1 allele respond to environmental pulmonary toxicants. Researchers recently reported finding high levels of Fmo1, and low levels of Fmo2 and Fmo3 in mouse lung, in contrast to our own preliminary findings that Fmo2 was abundant in lung, Fmo3 mRNA levels were moderate and Fmo1 levels were low. This study was designed to determine whether differences in diet were responsible for these discrepancies, and to define parameters involved in regulation of mouse Fmo1, Fmo2 and Fmo3 mRNA in lung and liver. Mouse age and strain were chosen to match the study reported by Janmohamed et al. (2004). Eight female and eight male 129 S/V three week old weanlings were fed AIN93G, a semi-synthetic diet; or NIH31, a chow-based diet (n = 4) for five weeks. Total RNA was isolated and reverse transcribed from lung and liver tissues. Fmo1, Fmo2, Fmo3 and actin mRNA levels were determined using quantitative real-time PCR. We postulated that in mice fed AIN93G, Fmo2 would be the predominant isoform expressed. By contrast, patterns observed were greater abundance of Fmo1 than Fmo2 in lung and liver regardless of diet. However, due to the high variability found in the data further confirmation is required. Additional studies to examine the influence of mouse strain and age will be necessary to determine if these factors are responsible for observed differences in mRNA levels.