Serotonin (5-HT) has been shown to act as a morphogen in craniofacial and heart development and in the migration of neural crest derivatives. Some of these structures are capable of capturing 5-HT during development, but nothing is known about the localization of the main monoamine degradation enzymes, monoamine oxidase (MAO) A and B, in these developing tissues. We generated a highly specific antibody to MAOB; immunoreactivity is entirely abolished in brain extracts or brain sections of mice lacking MAOB. From the use of this antibody and specific riboprobes, we report that MAOB is expressed early in a variety of neural crest derivatives, in facial sensory organs, and in the heart. From E11.5 to P0, MAOB was found to be strongly expressed in the following neural crest derivatives: the aorta, cranial mesenchyme (developing bones, sensory neurons of the cranial ganglia, cartilages, thyroid, and striate muscles), dental mesenchyme, several soft palate derivatives, and boundary cap cells (E11.5-P4). Boundary cap cells contribute to the formation of nerve exit-entry points between the central and the peripheral nervous systems. Several facial sensory organs also contained MAOB mRNA, protein, and activity. High MAOB expression was noted in the olfactory placode, the dorsal part of the olfactory epithelium, the olfactory nerve layer (probably the ensheathing glia), the cochlear ganglionic cells, the taste buds, and the Merkel cells in the vibrissae follicles. Finally, we found that MAOB is massively expressed in the pharyngeal organ, heart, liver, and mast cells. In contrast, MAOA expression was restricted to the sympathetic ganglia and to the meningeal and capillary blood vessels. The pattern of MAOB expression generally matched the previously reported patterns of expression of the plasma 5-HT transporter expression or of the histamine biosynthetic enzyme L-histidine decarboxylase, suggesting a role for MAOB in fine regulation of the levels of 5-HT and histamine in the developing embryo.