Kidney transplantation is the most efficient method of renal replacement therapy. When this method is performed, native urinary bladder is the preferred urinary reservoir. However, in some patients with an anatomically and functionally abnormal lower urinary tract, the urinary bladder cannot be used for transplantation. In these patients, urinary diversion should be performed before kidney transplantation. We present a case of a 32-year-old male patient with orthotopic kidney transplantation performed using a colon pouch (Mainz-pouch III). He was born with severe anomalies including sacral agenesis, anorectal atresia, and hypospadias, which were corrected during childhood. Neurogenic bladder with severe vesicoureteral reflux led to end-stage renal disease. This dysfunctional bladder was unsuitable for kidney transplantation, and a staged approach for future transplantation was chosen. The first step was the creation of urinary diversion. Due to a short appendix, we created a continent, colon pouch (Mainz pouch III). Two years later, orthotopic kidney transplantation was performed using a right cadaveric kidney. The renal vessels were anastomosed to the aorta and inferior vena cava and the pyelon to the native ureter. Four years after transplantation, the patient has stable renal function without any complications. This is the first documented case of using Mainz-pouch III as a reliable option for kidney transplantation in selected patients.