In Drosophila, evolutionarily conserved transcription factors are required for the specification of neural lineages along the anteroposterior and dorsoventral axes, such as Hox genes for anteroposterior and columnar genes for dorsoventral patterning. In this report, we analyse the role of the columnar patterning gene ventral nervous system defective (vnd) in embryonic brain development. Expression of vnd is observed in specific subsets of cells in all brain neuromeres. Loss-of-function analysis focussed on the tritocerebrum shows that inactivation of vnd results in regionalized axonal patterning defects, which are comparable with the brain phenotype caused by mutation of the Hox gene labial (lab). However, in contrast to lab activity in specifying tritocerebral neuronal identity, vnd is required for the formation and specification of tritocerebral neural lineages. Thus, in early vnd mutant embryos, the Tv1-Tv5 neuroblasts, which normally express lab, do not form. Later in embryogenesis, vnd mutants show an extensive loss of lab-expressing cells because of increased apoptotic activity, resulting in a gap-like brain phenotype that is characterized by an almost complete absence of the tritocerebral neuromere. Correspondingly, genetic block of apoptosis in vnd mutant embryos partially restores tritocerebral cells as well as axon tracts. Taken together, our results indicate that vnd is required for the genesis and proper identity specification of tritocerebral neural lineages during embryonic brain development of Drosophila.