Chemical genomics is a new and rapidly developing field. It refers to the use of cell-permeable small molecules, which are highly specific for their protein targets, in order to dissect biological pathways and to discover new drug leads. Small-molecule screening is usually limited to high-throughput approaches that use defined cell lines; however, whole organism screening is gaining increasing attention. This review addresses the latter concept and highlights the advances in whole organism-based screening, with an emphasis on the use of the zebrafish (Danio rerio).