Whole-mount in situ hybridization (WISH) is a method to visualize gene expression within a whole organism. Although it is an essential approach in developmental biology to describe the gene expression patterns during embryogenesis, the simultaneous processing of numerous embryos in a large-scale experiment such as a screening assay has been difficult for an individual due to the limited capacity of the experimental setting. This chapter describes the optimal protocol for a WISH assay in a relatively large experimental scale, which allows for more efficient processing of embryos. The major improvement in the efficiency has been achieved by the several refinements such as the introduction of a quick method for probe synthesis, the use of mesh-buckets to facilitate handling samples, and the simplification of the conventional procedures. In combination with publicly accessible gene expression databases, WISH assays will be more favorable for a large-scale assay using mouse embryos.