Vertebrate embryos exhibit a striking midline axis of symmetry that can be recognized in the overall body plan, the framework of skeletal structures and the organization of the nervous system. Cells located at the midline of the embryo during gastrulation have a crucial influence on the establishment of cell identity and pattern within the nervous system. The identification of transcription factors and secreted proteins that are expressed by these midline cell groups has begun to provide a molecular characterization of the organizing centers that establish early neural identity and pattern.