Congenital abnormalities of the kidney and urinary tract, CAKUT are common in humans, occurring at a frequency of approximately 1 in 500 fetal ultrasound examinations. CAKUT are major causes of chronic renal failure in infants and young children, but little is known about the molecular pathogenesis of these disorders. To date, several gene mutations have been identified as a cause of human CAKUT: these include PAX2, KAL, EYA1, AGTR2 and HNF-1β. At present, there is only limited information regarding how mutations alter gene expression during development to cause some CAKUT. The most convincing information comes from the multiorgan malformation syndromes with specific gene mutations. However, these syndromes are relatively rare, and most CAKUT appear to occur in isolation. The goal of this review is to provide an overview of these genetic disorders for CAKUT. An understanding of the genetic aspects of human CAKUT will help to unravel the pathogenesis of these disorders and may facilitate the design of genetic screening tests for early diagnosis and appropriate genetic counseling. Moreover, a deeper insight into the relationship between abnormal genes and the pathogenesis of abnormalities of CAKUT will provide an etiological classification of CAKUT. In addition, the importance of developing a registry of patients with various forms of CAKUT is discussed. This information will allow us to combine molecular biology and classical epidemiologic methods, and to continue expanding our knowledge regarding CAKUT.