Optically transparent zebrafish embryos provide an excellent vertebrate model system in which to reveal specific mRNA and protein expression patterns during development. Whole-mount preparations can be used to generate three-dimensional color or fluorescent readouts of the expression pattern of a given gene (or genes), matched with a bright-field image of all the tissues in the developing embryo. Whole-mount mRNA in situ hybridization (WISH) has long been the method of choice for revealing gene expression patterns in zebrafish because this method depends only on being able to identify a relatively short region of nucleotide sequence unique for the gene of interest. In contrast, the scarcity of antibodies that are specific to or cross-react with zebrafish proteins has limited the widespread use of immunocyto-chemical applications, though this situation will improve in the future. The elucidation of the specific expression patterns of Wnt pathway genes in zebrafish has made a major contribution to our current understanding of their roles in vertebrate development.