Nkx homeobox transcription factors are expressed in diverse embryonic cells and presumably control cell-type specification and morphogenetic events. Nkx2-9 is a novel family member of NK2 genes which lacks the conserved TN-domain found in all hitherto known murine Nkx2 genes. The prominent expression of Nkx2-9 in ventral brain and neural tube structures defines a subset of neuronal cells along the entire neuraxis. During embryonic development, Nkx2-9-expressing cells shift from the presumptive floor plate into a more dorsolateral position of the neuroectoderm and later become limited to the ventricular zone. Nkx2-9 expression overlaps with that of Nkx2-2 but is generally broader. While initially Nkx2-9 is expressed in close proximity to sonic hedgehog, its expression domain clearly segregates from sonic hedgehog at later developmental stages. The dynamic expression pattern of Nkx2-9 in ventral domains of the CNS is consistent with a possible role in the specification of a distinct subset of neurons. Copyright 1998 Elsevier Science Ireland Ltd.