Renal malformations are the major cause of renal failure during early childhood. They are found in approximately 100 genetic syndromes. We review the embryologic development of the kidney and its molecular control. Important new information has been derived from mutational analysis in humans and mice. We describe how mutations in nine transcription factors, 12 signaling molecules and nine gene products involved in a variety of other cellular functions disrupt renal morphogenesis. The information presented provides a template for integrating new discoveries on the molecular basis of renal development, for classifying renal malformations observed in the clinical setting, and for identifying defective genes in affected patients.