The article describes an extremely rare congenital anomaly of the male genitourinary tract – a cyst of the right ureterovesical junction associated with the absence of the right kidney, probably caused by abnormal development of the Wolffian duct and ureteric bud. A 35-year-old man had a one-year history of progressive dysuria. Contrast computed tomography revealed agenesis of the right kidney, cystic dilatation of the intramural segment of the right ureter projecting into the bladder, as well as tortuosity and atresia of the proximal ureter; the left kidney and ureter were normal. The patient underwent laparoscopic right ureterectomy with transurethral exploration of the bladder and placement of a left ureteral stent. Histopathological examination confirmed a cyst of the ureterovesical junction with chronic inflammation and changes in the cystic wall. The postoperative course was uneventful. The case highlights a rare developmental anomaly related to the Wolffian duct, distinct from Zinner syndrome, and the importance of recognizing atypical manifestations for accurate diagnosis and surgical management.