About one in forty babies is born with a recognisable congenital anomaly at birth. Rapid progress is being made in recognising the genetic contribution to these defects. From over 2000 likely single gene malformation syndromes in humans the gene has been isolated or mapped in about 10%. Despite the availability of animal models, the study of malformations in humans continues to reveal novel genes and unpredicted functions for known genes. The importance of the study of clinical malformations to the understanding of embryological development in humans and other organisms is discussed and reviewed.