The raphe nuclei are distributed near the midline of the brainstem along its entire rostro-caudal extension. The serotonergic neurons are their main neuronal components, although a proportion of them lie in subdivisions of the lateral reticular formation. They develop from mesopontine and medullary primordia, and the resulting grouping into rostral and caudal clusters is maintained into adulthood, and is reflected in the connectivity. Thus, the mesencephalon and rostral pons, neurons within the rostral raphe complex (caudal linear, dorsal raphe, and median raphe nuclei) project primarily to the forebrain. By contrast, in the caudal pons and medulla oblongata, neurons within the caudal raphe complex (raphe magnus, raphe obscurus, raphe pallidus nuclei and parts of the adjacent lateral reticular formation) project to the brainstem nuclei and to the spinal cord. The median raphe and dorsal raphe nuclei provide parallel and overlapping projections to many forebrain structures with axon fibers exhibiting distinct structural and functional characteristics. The caudal group of the serotonergic system projects to the brainstem, and, by three parallel projections, to the dorsal, intermediate and ventral columns in the spinal cord. The serotonergic axons arborize over large areas comprising functionally diverse targets. Some projections form classical chemical synapses while many do not, thus contributing to the so-called paracrine or volume transmission. The serotonergic projections participate in the regulation of different functional (motor, somatosensory, limbic) systems; and have been associated with a wide range of neuropsychiatric and neurological disorders. Finally, recent experimental data support the role of serotonin in modulating brain development, such that a dysfunction in serotonergic transmission during early life could lead to long lasting structural and functional alterations.