Confocal laser scanning reflection microscopy (CLSM) in combination with whole-mount in situ hybridization (WMISH) is a novel method to visualize gene expression patterns in three dimensions in whole embryos. The method uses conventional NBT/BCIP precipitation by alkaline phosphatase in WMISH samples and confocal detection by reflection microscopy. WMISH protocols can also be combined with fluorescent counterstainings such as DAPI, antibodies, GFP lines, and fluorescent in situ probes. Such double and triple labeling combined with confocal microscopy allows expression profiling at a cellular resolution in cell types or embryological structures of interest. Whole-mount reflection CLSM will thus greatly facilitate large-scale, cellular resolution expression profiling in vertebrate and invertebrate model organisms. more