In Drosophila, specification of neural identity requires a network of conserved transcription factors, such as the columnar genes for dorsoventral patterning. Here, we analyze the expression and function of the columnar patterning gene muscle specific homeobox (msh) in late embryonic brain development. Expression of msh is observed in all brain neuromeres, including neurons and neuropile glia. Functional analysis demonstrates that msh is essential for proper development of the tritocerebral neuromere and brain neuropile glia. Thus, msh mutants display a severe loss of neural and glial tissue together with axonal patterning defects. This gap-like phenotype initially correlates with defects in neural and glial cell formation and during later embryonic development is associated with increased apoptotic activity. Taken together, our results provide evidence that the columnar patterning gene msh is required for correct tritocerebral neuromere development, as well as for neuropile glia formation and axogenesis in embryonic brain development of Drosophila. Developmental Dynamics 235:2920 -2929, 2006.