Ectopic kidneys are frequently associated with primary renal dysplasia or a disturbance of urine transport. Sacral agenesis is defined by the absence of two or more bodies of the lower vertebral and is often associated with a neurogenic bladder dysfunction. A 5-year-old boy with sacral agenesis and a right-sided cake kidney, presented with progredient renal failure caused by recurrent urinary tract infections, incomplete bladder emptying and vesicorenal reflux. After extensive diagnostics, the anatomical situation was explored by laparotomy to find a solution for this complex situation. Despite modern diagnostic tools, the preoperatively estimated renal function of the cake kidney was incorrect. After resecting of the right collecting system and refluxing megaureter out of the cake kidney, anti-refluxive implantation of the left ureter into the bladder was performed and the megacystis was treated by detrusor duplication. After three years, the now 8-year-old boy voids residual free without any signs of urinary tract infection. Renal function and proteinuria have improved. The only medication required is nifedipine (20 mg twice a day) for treatment of the renal hypertension.