The zebrafish (Danio rerio) has been widely utilised for the study of developmental biology, which has lead to the evolution of sophisticated cellular and molecular approaches. More recently, the rapid progress of various zebrafish genomic infrastructure initiatives is facilitating the development of zebrafish models of human disease. This review aims to describe several representative examples of how the zebrafish can be successfully used to identify novel genes and assign gene function, providing invaluable clues to human pathophysiology.