Monoamine oxidases A and B (MAOA and MAOB) are the major catabolic isoenzymes of catecholamines and serotonin in the mammalian brain. Although the distribution of the monoamine oxidase protein has been mapped by ligand binding and immunohistochemistry, the sites of MAOA and MAOB synthesis have not been precisely determined. In this study, we used in situ hybridization to visualize MAOA and MAOB mRNAs in the rat brain by using specific cDNA and oligonucleotide probes. MAOA mRNA was localized in major monoaminergic cell groups, such as the dorsal vagal complex, the C1/A1 groups, the locus ceruleus, the raphe nuclei, the substantia nigra, and the ventral tegmental area. MAOA mRNA was also found in forebrain structures, such as the cortex, the hippocampus, the thalamus, and the hypothalamus. In contrast to the distribution of MAOA mRNA, high levels of MAOB mRNA were present in only three brain regions: the area postrema, the subfornical organ, and the dorsal raphe. The in situ visualization of MAO mRNA demonstrates that MAOA mRNA synthesis is wide spread in many catecholaminergic and serotonergic cell groups, whereas MAOB mRNA synthesis is far more discrete and limited. The different expression patterns of MAOA and MAOB suggests that may also have different physiological functions.