SYNOPSIS. It has long been recognized that the notochord, a derivative of the gastrula organizer, is important for patterning the vertebrate embryo. Experimental manipulations of amphibian and chick embryos demonstrate the notochord's influence on neural tube and somite differentiation. Recent studies implicate the notochord-derived signal Sonic hedgehog. In zebrafish, genetic strategies have enabled the recovery of mutations that disrupt notochord development. Embryos mutant for floating head or no tail lack differentiated notochord and, consistent with encoding transcription factors, both genes behave cell autonomously in genetic mosaics: wild-type cells develop into notochord in mutant embryos, whereas mutant cells fail to contribute to wild-type notochord. In floating head mutants, axial mesoderm fated to form notochord respecines to paraxial mesoderm, differentiating into muscle instead. As a result, fused somites develop across the trunk midline. In no tail mutants, mesenchymal cells related by lineage to notochord are found in the midline, and although trunk somites are bilaterally paired, they lack Engrailed-expressing muscle pioneer cells. In the presence of wild-type notochord, however, no tail mutant cells can differentiate muscle pioneers, suggesting that induction of muscle pioneers is a normal function of notochord. Notochord is also involved in induction of floor plate at the ventral midline of the vertebrate neural tube; yet in floating head and no tail mutants, floor plate cells develop in the absence of differentiating notochord. Expression of sonic hedgehog by newly-forming axial mesoderm at gastrulation may account for floor plate induction prior to notochord differentiation. Thus, analyses of zebrafish notochordless mutants suggest a role for both early and late signaling by cells of the notochord lineage during embryogenesis.