Seventeen patients with urolithiasis in problem kidneys which comprised horseshoe kidneys, medullary sponge kidneys (MSKs), polycystic kidneys and duplex kidneys presented to our hospital and were evaluated for treatment with extracorporeal shock-wave lithotripsy (ESWL). A total of 21 renal units were treated with ESWL. Auxiliary procedures included preoperative retrograde ureteral catheterization (1 horseshoe kidney) placement of a retrograde double-J catheter stent (1 MSK), percutaneous nephrolithotomy (PCNL; 2 MSKs) and postoperative PCNL (1 MSK). The outcome showed that 5 renal units (23.8%) were stone free, 15 renal units (71.4%) had a decreased stone load with residual sotne and improved symptoms, and 1 renal unit (4.8%) had residual stone with persistent symptoms. We conclude that ESWL can be used as a primary management tool for calculi in problem kidneys.