Background A supernumerary kidney (SK) is an additional kidney with its own capsule and blood supply that is not fused with the ipsilateral kidney (IK). Because individual case reports indicate a high morbidity rate, the aim of this retrospective study was a detailed analysis of this rare anatomical variant. Methods Our systematic imaging-based search for SKs, conducted in the period from 2000 and to 2017, yielded 9 cases in total (5 men, 4 women; mean age: 51.8 ± 22.8 years). Results The SKs were observed on the right in six and on the left side in three cases. In six subjects (66%) they were located caudal and in three cases (33%) cranial to the ipsilateral kidney. Calculi were found in three (33%) of the renal collecting systems. Five (56%) of the SKs had hydronephrosis grade IV and one SK had recurrent pyelonephritis (11%). Two of the ureters opened into the ipsilateral seminal vesicle (22%). Two (22%) SKs were functional but atrophic. Clinically relevant findings were made in 33% of the IKs: atrophy (n = 2), calculi (n = 1), and reflux with recurrent pyelonephritis (n = 1); another 33% had anatomical anomalies without functional impairment. The correct diagnosis of a SK is possible using CT imaging in all subjects. The prevalence of SK based on CT imaging can be estimated to be 1:26750. Conclusions CT is the method of choice for visualizing SKs. The correct diagnosis is crucial in preventing dispensable surgical procedures and for providing optimal patient treatment and outcome.