The complex vertebrate nervous system has evolved from a simpler nervous system such as that seen in present-day protochordates. Through a recent accumulation of gene-expression data, together with fine anatomical studies, we are now able to identify both how the neural tube was patterned when it first evolved and what is truly novel in the vertebrate neural tube. We are entering a new era in the understanding of how the evolution of novel vertebrate structures is linked to genetic evolution.