Retrograde intrarenal surgery (RIRS) in patients with horseshoe kidneys (HSKs) remains poorly studied. The present study aimed to assess clinical success and stone-free rates in HSK patients with renal stones treated with flexible ureteroscopy. RIRS was attempted in 20 patients with 25 renal stones in HSK from December 2008 to January 2012. The patients were evaluated with imaging studies including plain abdominal radiography, intravenous urogram, abdominal ultrasonography or non-contrast tomography scan. Success rate was defined as stone-free or residual fragment less than 4 mm. Pre-operative, operative and postoperative data were retrospectively analyzed. A total of 20 patients were included in the present study (12 males, 8 females). 9 of 25 renal stones (36 %) were located in the lower calyx of the kidney, whereas 7 (28 %) in the middle calyx, 5 (20 %) in the renal pelvis and 4 (16 %) in the upper calyx. The mean stone size was 17.8 +/- 4.5 mm. The stone-free rate was 70 % after a single procedure. 6 patients required shock wave lithotripsy and two of these were completely stone-free. Average hospital stay was 1.4 +/- 0.7 days. Minor complications as classified by Clavien I or II occurred in 25 %. No major complications (Clavien III-V) occurred in the study group. RIRS is an effective and safe treatment modality for renal stones in patients with HSK. The procedure has minimal morbidity and high success rate.