The aim of this study was to compare the outcomes of retrograde intrarenal surgery (RIRS) and miniaturized percutaneous nephrolithotomy (mini-PNL) in management of lower-pole renal stones with a diameter smaller than 15 mm. Between December 2009 and July 2012, the patients with the diagnosis of lower-pole stones were evaluated by ultrasonography, intravenous pyelography and computed tomography. The records of 73 evaluable patients who underwent mini-PNL (n = 37) or RIRS (n = 36) for lower-pole (LP) stones with diameter smaller than 15 mm were reviewed retrospectively. Of the 73 patients, 37 underwent mini-PNL and 36 underwent RIRS. The stone-free rates were 89.1 and 88.8 % for mini-PNL and RIRS groups, respectively. The mean operation time was 53.7 ± 14.5 in the mini-PNL group but 66.4 ± 15.8 in the RIRS group (P = 0.01). The mean fluoroscopy times and hospitalization times were significantly higher in the mini-PNL group. There was no major complication in any patient. RIRS and mini-PNL are safe and effective methods for treatment of LP calculi with a diameter smaller than 15 mm. RIRS is a non-invasive and feasible treatment option, and has also short hospitalization time, low morbidity and complication rate. It may be an alternative of mini-PNL in the treatment LP calculi with smaller than 15 mm.