Horseshoe kidneys are the most common renal fusion anomalies. Ureteropelvic junction obstruction, urolithiasis and renal malignancies are the most common complications that occur in this patient population. Endourological management of these complications has decreased perioperative morbidity. We identified the applications of minimally invasive surgery for treating complications secondary to horseshoe kidney. A comprehensive literature review of the different endourological approaches in the management of complications secondary to horseshoe kidney was performed using MEDLINE. Ureteropelvic junction obstruction can be managed by percutaneous endopyelotomy or laparoscopic pyeloplasty with good results. Small stones associated with horseshoe kidney are best managed by shock wave lithotripsy, while stones that have failed management by shock wave lithotripsy or are greater than 2 cm. are best managed percutaneously. All patients should undergo metabolic evaluation. Ureteroscopy or shock wave lithotripsy is associated with a higher residual stone rate than the percutaneous approach. Laparoscopic nephrectomy is a safe and feasible option for benign and malignant horseshoe kidney diseases. Endourological techniques can be safe and effective for treating complications secondary to horseshoe kidney.