Congenital anomalies of the kidney and urinary tract (CAKUT) occur in approximately 1 in 500 foetal ultrasound examinations. The CAKUT phenotype can involve varying degrees of renal dysplasia, renal hypoplasia, urinary tract obstruction, ureteropelvic anomalies such as megaureter, ureteral atresia, ectopic ureteral orifice, and duplex collecting system The nephrogenic (mesenchymal) and the ductogenic (ureteric) events are regulated by transcription factors, proto-oncogenes and growth factors in a complex fashion. Dysregulation of specific molecular pathways has been implicated as a primary mechanism for CAKUT. This review will attempt to clarify the molecular basis of CAKUT by focusing on these key developmental pathways. First, however, an examination of normal metanephric kidney development is necessary. Furthermore, clinical aspects of CAKUT, including prenatal diagnosis and current treatments, will be introduced. Through the critical evaluation of a range of diverse scientific literature, it is hoped that an overview of the current status of this important area of developmental anatomy is achieved.