FMO1 and FMO3, the main FMOs described in the rat, are highly expressed in the liver and the kidney. The age, from 3 to 11 weeks, and gender-dependent expression of FMO1 and FMO3 in the rat liver and kidney were investigated. Based on the enzyme activities, protein levels and mRNA levels, this study demonstrates an important increase in the expression of the FMO3 in the liver of male rats during a period that corresponds to the acquisition of the sexual maturity. Rat liver FMO1 remains unchanged during this period of observation. The evolutions of both isoforms in the kidney of the male rat are similar to those observed in the liver. On the contrary, the important decrease in the total flavin-containing monooxygenase (FMO) activity observed in the liver of female rat is linked to a considerable decrease in the FMO1-dependent activity, FMO1 protein and FMO1 mRNA levels as a function of age. The expression of the FMO3 in the liver does not seem to be affected by the age of the female rat. Inversely, the expression of FMO1 in the female rat kidneys does not seem to be modified as a function of age while the expression of FMO3 is strongly increased.