An important question in neurobiology is how different cell fates are established along the dorsoventral (DV) axis of the central nervous system (CNS). Here we investigate the origins of DV patterning within the Drosophila CNS. The earliest sign of neural DV patterning is the expression of three homeobox genes in the neuroectoderm-ventral nervous system defective (vnd), intermediate neuroblasts defective (ind), and muscle segment homeobox (msh)-which are expressed in ventral, intermediate, and dorsal columns of neuroectoderm, respectively. Previous studies have shown that the Dorsal, Decapentaplegic (Dpp), and EGF receptor (Egfr) signaling pathways regulate embryonic DV patterning, as well as aspects of CNS patterning. Here we describe the earliest expression of each DV column gene (vnd, ind, and msh), the regulatory relationships between all three DV column genes, and the role of the Dorsal, Dpp, and Egfr signaling pathways in defining vnd, ind, and msh expression domains. We confirm that the vnd domain is established by Dorsal and maintained by Egfr, but unlike a previous report we show that vnd is not regulated by Dpp signaling. We show that ind expression requires both Dorsal and Egfr signaling for activation and positioning of its dorsal border, and that abnormally high Dpp can repress ind expression. Finally, we show that the msh domain is defined by repression: it occurs only where Dpp, Vnd, and Ind activity is low. We conclude that the initial diversification of cell fates along the DV axis of the CNS is coordinately established by Dorsal, Dpp, and Egfr signaling pathways. Understanding the mechanisms involved in patterning vnd, ind, and msh expression is important, because DV columnar homeobox gene expression in the neuroectoderm is an early, essential, and evolutionarily conserved step in generating neuronal diversity along the DV axis of the CNS.