The zebrafish has emerged as a powerful model organism for the experimental interrogation of the processes that bring about vertebrate development. In this thesis we study functions of Hedgehog (Hh) signaling, a process that is frequently dysregulated in cancer, that occur during the formation of the zebrafish embryo. First, we investigate a possible link between Hh signaling and the directed migration of germ cells to the presumptive gonad in the early embryo and find that Hh-targeting drugs can perturb germ cell migration, but Hh signaling itself does not regulate this process. Second, we study the formation of motoneurons in the developing ventral spinal cord and find that Hh signaling and retinoic acid signaling work together to induce these cells by the same downstream output of Gli transcription factor activity. Third, we generated transgenic zebrafish that reliably report Hh signaling events at multiple levels of the pathway and we apply these tools in initial studies of zebrafish regeneration. In summary, these studies further our knowledge of the roles for Hh signaling in vertebrate development and will lead insight into the pathology of Hh-related disorders.