Congenital anomalies of the kidney and urinary tract (CAKUT) occur at a frequency of 1 in 500 live births and are a common cause of renal insufficiency in childhood. CAKUT encompass a wide spectrum of malformations including anomalies of the kidney, collecting system, bladder and urethra. Most cases of CAKUT are sporadic and limited to the urinary tract, but some of them are syndromic or associated with positive family history. To understand the basis of human renal anomalies, knowledge of kidney and urinary tract development is necessary. This process is very complicated, requires precise integration of a variety of progenitor cell populations of diverse embryonic origins and is controlled by many factors at every stage of development. This review focuses on the genetic factors leading to developmental errors of important morphogenetic processes, particularly in metanephric kidney induction and ureteric bud branching. The essential results of genetic studies in regard to CAKUT, performed on experimental models and in humans, are presented. However, further investigations are required to complete understanding of the complex molecular network, which will help us to determine novel preventive and therapeutic strategies for CAKUT.