Objective: This article reports our experience managing neoplasms, stenosis and urolithiasis in patients with anatomical variations of the urinary system, using an endourological approach, either with an antegrade access or with combined access. Patients and methods: A retrospective review was performed using medical records of all patients who underwent percutaneous endourological treatment at our institution between 2014 and 2019. Those with such urinary anatomical variations were selected. Results: Out of 185 patients, 10 were identified. The study group included patients with urinary diversion, renal transplantation and congenital anomalies. Patients were divided into two sets, A and B, based on the presence or absence of urolithiasis, respectively. In set A, the median operative time was 213 minutes (standard deviation ( SD)=65.91 minutes). Only one patient had lithiasis in the first postoperative evaluation. Two patients had postoperative complications graded ⩾II in the Clavien–Dindo classification. Regarding set B, the median operation time was 75 minutes ( SD=66.89 minutes). Two patients had postoperative complications graded ⩾II in the Clavien–Dindo classification. Conclusions: Patients with anatomical tract challenges currently have a longer life expectancy and are therefore prone to urological complications in their unusual structures. Treatment of urological complications is essential, and minimal invasive procedures should be considered to resolve them and to reduce morbidity. Level of evidence: Not applicable.