Anomalies of the urinary tract are the most common type of congenital anomalies. They occur as isolated changes or related to anomalies of the other organ systems in the body. Kidneys are most vulnerable subject to these anomalies; congenital renal anomalies comprise 60% of the causes of chronic kidney disease (CKD). Progression of this disease abridges kidney functions, and ultimately leads to chronic kidney failure (CKF). Detection of the oligomeganephronia and nephronophthisis in their early stages, as well as the treatment, decelerates the progression of damage to tissue, eliminates the occurrence of complications, and delays the onset of chronic renal failure. Drawing conclusions about the type of anomaly based solely on clinical features, laboratory reports and medical imaging, does not represent a reliable method. On the contrary, renal biopsy serves as more feasible diagnostic tool in assessing the nature of the disease, the degree, and the extent of the pathological changes. Most commonly used method is the ultrasound-guided percutaneous biopsy. The application of ultrasound provides an adequate view of intrarenal structures and collecting tissue samples in which the changes are most visible. A clear image of blood vessels and urinary canal system eliminates the possibility of their damaging. Preoperative preparation, proper techniques, and appropriate postoperative care reduce the risk of possible complications. In the case of contraindications for performing percutaneous biopsy, surgery is performed laparoscopically. Direct visual supervision of insertion of the probe inside the abdominal cavity, images of anatomical structures, and sample collection increase the efficiency of the laparoscopic method. A sample of tissue obtained by biopsy is then analyzed by light microscopy, immunofluorescence, immunohistochemistry, electron microscopy, and in situ hybridization. Pathohistological analysis of tissue obtained by biopsy confirms the diagnosis and evaluates the need for dialysis and transplantation for children with chronic kidney disease.