Treatment of calculi in patients with congenital renal anomalies (such as horseshoe, ectopic, autosomal dominant polycystic kidneys, and duplex systems) requires special considerations. These kidneys had abnormal vascular, altered calyceal orientation, and variable anatomical relations with the surrounding viscera. Nowadays, minimally invasive techniques (such as extracorporeal shock wave lithotripsy [SWL], flexible ureterorenoscopy [F-URS], percutaneous nephrolithotomy [PNL] and laparoscopic pyelolithotomy) are the most frequently used modalities for treatment of calculi in both normal and anomalous kidneys. They offer high stone-free rates with minimal morbidity and improved recovery. However, there are many challenges in utilization of these modalities in patients with renal anomalies.