The vertebrate nervous system forms by the specification of, successively, neuroepithelial regions and cell groups. One of the proposed major histogenic steps is the subdivision of the neural tube in compartments along its caudorostral and dorsoventral axis. This event is reflected, and may be directed, by the restricted expression of many transcription factors. Here, we report on the isolation of a new homeobox gene of the paired superclass, Otlx2, whose early expression pattern in the mesencephalon and prosencephalon is congruent with proposed neuromeric models of brain morphogenesis. In addition, its late embryonic and postnatal expression, in clear continuity with the earlier pattern, suggests a role in the neuronal differentiation and the histogenesis of several prosencephalic and mesencephalic areas. Finally, Otlx2 is expressed from the earliest morphogenetic events in the Rathke's pouch, the anlage of the adenohypophysis, an expression site shared by a very close homologue, Otlx1/Ptx1/P-Otx.