Aims: The management of kidney stones with congenital kidney anomalies andabnormal variations continue to pose challenges to urologists. The treatment optionsinclude open surgery, extracorporeal shock wave lithotripsy (ESWL), percutaneousnephrolithotomy (PCNL), laparoscopy and ureterorenoscopy (rigid or flexible).Methods: In this study, we retrospectively reviewed health records ofpatients with abnormal urinary tract anatomy due to both congenital oracquired reasons who were operated between January 2009 and July 2016.Results: The study included a total of 66 patients with anatomical abnormalities orsolitary kidney. These patients had various congenital or acquired abnormalities.Fifty-four patients were stone free after the first intervention, and the initial operationswere successful. Two patients with horseshoe kidney had severe bleeding, andthe operation was canceled. One of these two patients underwent PCNL surgery.Conclusions: In recent years, endoscopic stone surgery has gained increasing popularitydue to improved techniques. The most important development in this area was in F-URSand retrograde intrarenal surgery. However, current literature is limited regarding patientswith urinary tract abnormalities. Our results demonstrate that F-URS seems to be a safeand effective procedure for urinary tract anatomical variations. However, studies involvinglarger patient series would yield more information.