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Background Urolithiasis is a frequent complication in a heterotopic reservoir and the surgical management could be a difficult problem. Open surgery is not recommended in patients with multiple previous surgeries. A less invasive technique, such as the endourologic procedures, would allow high stone-free rate and low surgical morbidity. Introduction Stone formation in the reservoir is a well-known complication of urinary diversion. The incidence of lithiasis in patients with continent urinary diversion is reported as 12–52.5%. Most patients will have multiple physical factors, such as immobility, need for self-catheterization and poor urine drainage, so that it is not certain that an intestinal reservoir is the cause of stones on its own. The management of urolithiasis in continent urinary diversion can be challenging and could be a difficult problem to solve. A less invasive technique, such as the endourologic procedures, is desiderable, especially in patients with kidney transplant and low immune defence. Materials and Methods We present the case of a 59-year-old woman with previous history of spina bifida and with neurogenic bladder. At a pediatric age, she underwent incontinent urinary diversion using a sigmo-colic conduit. For several years she had been suffering from kidney stones and recurrent urinary infections, which led to a left nephrectomy for pyonephrosis, subsequent deterioration of renal function and dialysis. In 2004, we performed an atypical continent and self-catheterizable reservoir using the previous colic conduit detubularized and ileum-cecal tract with Mitrofanoff system conduit of 14 Fr size. Finally, kidney transplant was carried out as last surgical procedure. Recently she has come to our attention for multiple and large reservoir stones. Surgical Technique preliminary exploration of the continent pouch with flexible cystoscope. Percutaneous access with Endovision° direct control through the afferent conduit with 8 Fr flexible ureteroscope. Dilation of percutaneous tract with pneumatic baloon and positioning 30 Fr Amplats sheet. Lithotripsy, with ultrasound and ballistic sources, was performed and the residual fragments were removed with grasping. At the end of the procedure, after controlling the complete clearance with flexible nephroscope and X-ray a percutanous 12 Fr catheter and a 12 Fr Foley in the Mitrofanoff conduit were inserted. Results No fever or increase serum creatinine were observed in the post-operative time. On day 3, we removed the percutaneous foley and after 7 days we performed a cystography with a normal pouch configuration; no leakage or residual fragments were observed. The woman was discarge and returned to usual self-catheterization. The first 3-month post-operative control was regular; no infections or pain were reported. Conclusions In special cases, like this one, the percutaneous procedure is preferred to open surgery for a best control of the pouch and a simple complete clearence of the fragments.