Due to the presence of structural and anatomical differences that accompany anomalous kidneys, currently available endourological modalities such as SWL and PNL may be insufficient, or additional laparoscopic assistance may be required. The present study aims to evaluate the efficacy and safety of retrograde flexible ureterorenoscopic stone treatment in patients with kidney anomalies. Over the last 3 years, 25 patients with renal stones in anomalous kidneys were consecutively treated by flexible ureterorenoscopy and holmium:YAG laser lithotripsy. Among the 25 patients, fiberoptic or digital flexible ureterorenoscopies were performed for the management of horseshoe kidneys (n = 3), cross-fused ectopic kidney (n = 1), renal ectopies [n = 13; associated with pelvic (n = 6) or lumbar kidneys (n = 7)], renal malrotations (n = 4), and duplicate ureters (n = 4). For lithotripsy, 200 or 273 µm probes were used, and for stone retraction 1.3-1.9 Fr ZeroTip baskets were used. Success was defined as the complete absence of stones as evaluated with a CT scan 1 month after the operation. The mean patient age was 39.4 ± 15.75 years, and the mean stone size was 194.64 ± 103.93 mm(2) (range 50-393). Complete stone clearance was achieved in 16 patients (64%) after a single session. Seven of the patients with residual stones underwent a second session and the remaining three patients were subsequently treated with SWL. The overall complete clearance rate was 88% (22 patients) with ancillary procedures. There were no serious postoperative complications except for one case (4%) of urosepsis. Flexible ureterorenoscopy with holmium laser lithotripsy is a safe option for the treatment of renal stones in anomalous kidneys with satisfactory success rates.