The zebrafish (Danio rerio) emerged as a valuable model to discover genes controlling vertebrate development, owing to its amenability to mutagenesis and unbiased phenotype-based screens. The transparency of early developmental stages enables morphological changes to be readily detected in many organs and tissues types, including the central nervous system. The same attribute makes embryonic and larval zebrafish well suited for cataloging spatial patterns of gene expression and for time-lapse imaging of fluorescently labeled cells. The application of mobile transposable elements and, more recently, CRISPR/Cas 9 targeted genome editing has expedited the production of transgenic animals. This has advanced techniques to visualize neuronal populations and their axonal projections, to selectively destroy them, or to manipulate their synaptic activity. Neural activation in specific regions or throughout the brain of live, behaving larvae can be monitored by transgenic strategies that capitalize on genetically encoded calcium indicators or voltage sensors. This chapter will outline how genetic and transgenic approaches have been applied to study left–right (L-R) asymmetry of the zebrafish epithalamic region of the brain, to learn how these differences develop, and to determine their impact on neural processing and behavior.