In spite of the fact that urologic surgical techniques used by urologists are becoming more and more minimally invasive and easier because of developing technologies, surgical approaches for the urinary stones in kidneys with abnormal anatomy are still confusing. The objective of this article is to determine the treatment options in these kidneys. For this purpose, between 2005 and 2015, we retrospectively evaluated patients operated for urolithiasis with various congenital renal anomalies in five referral urology clinics in our country. Of the 178 patients (110 male, 60 female), 96 had horseshoe kidneys, 42 had pelvic ectopic kidneys (PEKs), and 40 had isolated rotation anomalies (IRAs) of the kidney. We evaluated the patients for stone-free rate (SFR), mean operation time, mean hospitalization time, and complication rate. In horseshoe kidney, SFRs for retrograde intrarenal surgery (RIRS) and percutaneous nephrolithotomy (PNL) groups were 72.2% and 90%, respectively. In PEKs, these rates were 83.6% and 100% for RIRS and laparoscopic pyelolithotomy, respectively. SFRs in kidneys with IRA were 75% for RIRS and 83.3% for PNL. The mean operation time for RIRS and PNL groups in horseshoe kidney was 40.5 +/- 11.2 minutes and 74.5 +/- 19.3 minutes, respectively. In PEKs, these times were 52.1 +/- 19.3 minutes and 53.1 +/- 24.3 minutes for RIRS and laparoscopic pyelolithotomy, respectively. Mean operation time in kidneys with IRA was 48.7 +/- 14.4 minutes for RIRS and 53.2 +/- 11.3 minutes for PNL. Mean hospitalization times for RIRS and PNL groups in horseshoe kidneys were 1.4 +/- 0.7 days and 2.2 +/- 1.4 days, respectively. In PEKs, these times were 2.7 +/- 1.8 days and 1.9 +/- 0.4 days for RIRS and laparoscopic pyelolithotomy, respectively. Mean operation time in kidneys with IRA was 1.5 +/- 0.9 days for RIRS and 1.8 +/- 0.6 days for PNL. The results of our study showed that RIRS could be used in all of types of abnormal kidneys with small- and medium-sized renal calculi safely and satisfactorily. Copyright (C) 2017, Kaohsiung Medical University. Published by Elsevier Taiwan LLC.