Purpose We review our experience with percutaneous nephrolithotomy for stones in horseshoe kidneys when extracorporeal shock wave lithotripsy was unsuccessful or inappropriate because of stone burden. Materials and Methods Stone burden, nephrostomy and percutaneous surgical techniques, and clinical outcome of 12 consecutive patients undergoing percutaneous nephrolithotomy for calculi in horseshoe kidneys between 1988 and 1997 were reviewed. Results Complete stone removal was achieved by percutaneous methods alone in 9 patients (75%). More than 1 nephrostomy tract was required in 5 patients and additional intraoperative nephrostomies were necessary in 4. Flexible nephroscopy was essential in achieving complete stone removal in 9 of 11 patients (82%). Second look procedures for stone removal were required in 3 patients. No sepsis occurred and no transfusions were needed. Conclusions Percutaneous nephrolithotomy is a safe and effective method of stone removal in patients with calculi in horseshoe kidneys. Multiple nephrostomy tracts, the use of flexible nephroscopy and second look procedures may be necessary to achieve optimum stone removal.