Congenital anomalies of the kidney and urinary tract (CAKUT) represent 20% to 30% of all antenatally diagnosed fetal congenital anomalies in developed countries. CAKUT account for about 40–50% of children with chronic kidney disease. It is necessary to know the prevalence and pattern of these anomalies as well as genetic causes leading to these anomalies in order to take the appropriate steps in prevention and management, thereby reducing end-stage renal disease in society. Recent findings suggest that CAKUT may be caused by a multitude of different disease-causing genes. Lack of information about frequency of mutations in Indian children with CAKUT is a major barrier to the routine use of genetic testing in the clinic. Through our work, we plan to develop and standardize customized NGS based gene panel for mutation screening. The generated data will facilitate early detection and correct diagnosis, enable perinatal counseling and help identify markers that will help in prognostication. It will also establish a rapid, cheaper and effective diagnostic strategy for CAKUT mutation detection.