The ascidian larva has a central nervous system which shares basic characteristics with craniates, such as tripartite organisation and many developmental genes. One difference, at metamorphosis, is that this chordate-like nervous system regresses and the adult's neural complex, composed of the cerebral ganglion and associated neural gland, forms. It is known that neural complex differentiation involves two ectodermal structures, the neurohypophysial duct, derived from the embryonic neural tube, and the stomodeum, i.e. the rudiment of the oral siphon; nevertheless, their precise role remains to be clarified. We have shown that in Ciona intestinalis, the neural complex primordium is the neurohypophysial duct, which in the early larva is a short tube, blind anteriorly, with its lumen in continuity with that of the central nervous system, i.e. the sensory vesicle. The tube grows forwards and fuses with the posterior wall of the stomodeum, a dorsal ectodermal invagination of the larva. The duct then loses posterior communication with the sensory vesicle and begins to grow on the roof of the vesicle itself. The neurohypophysial duct differentiates into the neural gland rudiment; its dorsal wall begins to proliferate neuroblasts, which migrate and converge to build up the cerebral ganglion. The most anterior part of the neural gland organizes into the ciliated duct and funnel, whereas the most posterior part elongates and gives rise to the dorsal strand. The hypothesis that the neurohypophysial duct/stomodeum complex possesses cell populations homologous to the craniate olfactory and adenohypophysial placodes and hypothalamus is discussed. J. EXP. ZOOL. 304B, 2005. © 2005 Wiley-Liss, Inc.