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Congenital anomalies of the kidney and urinary tract (CAKUT) occur have an incidence of about 1% and they are one of the most common birth defects. CAKUT is the most common cause of end stage renal disease in children, leading to high morbidity and mortality in these patients. Recent studies indicate a strong genetic component in the determination of CAKUT. The genetic architecture of these malformations involves both point mutations and structural variants. The recent improvement in next-generation sequencing technologies resulted in a boost on discovery of new genes involved in CAKUT. Results from micro-array study have demonstrated that rare structural variants are an important source of genetic variation in patients with CAKUT. Moreover, these structural variants have been proven to be associated with developmental disorders that develop later in life, especially neurodevelopment diseases, such as autism, schizophrenia, epilepsy, intellectual disability, and others. The easy pre-natal diagnosis of CAKUT by ultrasound and the possibility of a rapid molecular diagnosis in a significant fraction of patients, implicate the kidney and urinary tract as new possible sentinels for other diseases that develop later in life, bearing strong implications for personalized medicine.