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Management of stone disease in an ectopic kidney is challenging. Laparoscopy or ultrasound guided percutaneous nephrolithotomy and retrograde intra-renal surgery are the preferred techniques for these stones. We performed ultrasound guided microperc using a 16 G needle for the management of renal calculi in pelvic ectopic kidneys in two patients. There was no intraoperative or post-operative complication. Both patients had complete stone clearance and were discharged on the first post-operative day. Ultrasound guided microperc is a safe and effective option for the management of small renal calculi in pelvic ectopic kidneys.