Segment polarity genes in Drosophila are required for the proper formation of epidermal pattern within each segment. Here we show that certain segment polarity genes are also critical for the determination of specific neuronal identities in the developing central nervous system (CNS) of the Drosophila embryo. For several mutants, however, the pattern defects do not simply parallel their cuticular phenotypes. In fused, armadillo, and cubitus interruptus Dominant mutants, much of the CNS appears relatively normal. In hedgehog mutants, the CNS is highly disorganized, but this disruption may occur secondary to the initial events of neurogenesis. The specific cellular defects in patched mutants suggests that this gene specifies a subset of neuroblasts and neural progeny underlying the region of epidermal pattern defect. gooseberry mutants display a complex series of alterations in neuronal identity both underlying and outside of the region of epidermal modification. Neuronal identities of a set of cells along the midline appear to be changed in Cell mutants. The phenotype of wingless mutants is the most restricted and may be due to improper communication between sibling neurons. Thus, in addition to their functions in epidermal pattern formation, at least four of the segment polarity genes (gooseberry, patched, Cell, and wingless) appear to have specific roles in the control of cell fates during neurogenesis.