During the development of the central nervous system, neurons are directed by both genetic and environmental factors to differentiate and form connections with their targets. We took advantage of the abundant homogeneous serotonergic innervations of the ependyma forming the supra- and subependymal plexuses to investigate possible commitment of embryonic neurons to innervate specific targets during axogenesis in the rat. The origin of the supraependymal innervation was determined by retrograde transport of cholera toxin (CT) from the ventricles. The supraependymal plexuses of the fourth ventricle mainly originated from neurons in the dorsocaudal region of the raphe dorsalis (DRN), while the rostral DRN and raphe centralis (CRN) contained perikarya projecting into the third ventricle. This suggested the existence, along the rostrocaudal axis of the raphe, of different neuronal subsets able to form distinct supraependymal plexuses in the third or fourth ventricle. To determine whether serotonergic neurons were committed to innervate specific areas of the ependyma, different embryonic metencephalic segments (rostral, median, or caudal) from 14-day-old rat embryos were independently grafted into the third or fourth ventricle of an adult brain in which the serotonergic neurons had been previously destroyed. The distinctive patterns of re-innervation specific to each of grafted segments indicate that subsets of embryonic serotonergic neurons are indeed committed to innervate certain restricted ependymal areas of the adult brain, presumably in response to different neurotropic and/or neurotrophic cues.