In the past decades zebrafish has been added to the group of vertebrate model organisms commonly used in genetic research. Based on its small size, external development, fast embryogenesis, transparent body and high fecundity zebrafish has quickly become a popular model in the fields of developmental biology, cell biology and pharmacology. Since the discovery of fluorescent proteins in vivo microscopy in zebrafish has become a widely used technique to observe cellular and molecular processes in the living organism. We use this combination of genetics and in vivo imaging to investigate the development and differentiation of the vertebrate brain and in particular the cerebellum. Here we aim to understand how migration and terminal differentiation of neurons is orchestrated on the cellular and molecular level. Furthermore, for investigating the initiation and progression of neurodegenerative diseases we develop zebrafish models that are amenable for in vivo diagnosis by bio-imaging. This will not only help to unravel the etiology of severe human diseases, but also offer routes for therapeutic intervention by means of small molecule screening.