The cell-, tissue-, sex- and developmental stage-specific expression profiles of five members of the flavin-containing monooxygenase (FMO) family, FMO1, 2, 3, 4 and 5, were investigated in 129/SV mice, using isoform-specific antisense RNA probes. In situ hybridization localized FMO1 and 5 mRNAs to the perivenous, and FMO 2, 3 and 4 mRNAs to the periportal, regions of the liver. In kidney, each FMO mRNA is localized to the distal and proximal tubules and collecting ducts; FMO1 mRNA is present also in the glomerulus. In lung, FMO1 and 3 mRNAs are expressed in the terminal bronchiole, and FMO1 mRNA also in the alveoli. FMO1 mRNA is present in neurons of the cerebrum and in the choroid plexus. RNase protection assays showed that the most abundant isoform in newborn liver, lung, kidney and brain, and in adult lung and kidney is FMO1, but in adult liver FMO5 is present in greatest amounts. In liver, lung and kidney, expression of Fmo1, 3 and 5 peaks at 3 or 5 weeks of age, but in the brain, Fmo1 expression is greatest in newborns. In the kidney, FMO5 mRNA abundance is fourfold greater in males than in females, at all stages of development. Our results demonstrate that Fmo1, 2, 3, 4 and 5 exhibit distinct cell-, tissue-, sex- and developmental stage-specific patterns of expression.