Genetic analysis in Drosophila and in the nematode C. elegans has led to the identification of many genes controlling all aspects of development, including development of the nervous system. Subsequent reverse genetic techniques have allowed the isolation of related vertebrate genes, and functional analysis, e.g. through misexpression experiments, or by inactivation through homologous recombination in mice has confirmed that these genes are indeed often required to control vertebrate development. In zebrafish, ,forward' genetic screens for mutations have been carried out that can be combined with molecular studies and experimental embryology, thus providing powerful means to study vertebrate development at all levels. Here, the identification and functional dissection of genes affecting development of the zebrafish nervous system is discussed, with an emphasis on genes affecting development of the midbrain-hindbrain boundary region. This region contains a population of cells acting to organize cell fate in the surrounding neural tube. Genetic analysis in mice and zebrafish begins to reveal the sequence of events and their underlying molecular mechanisms in development of the midbrain-hindbrain boundary region, from the time of induction to the formation of functional neuronal maps.