We report a case of pyonephrosis caused by a protein calculus in a patient on hemodialysis. A 56-year-old man had been treated with dialysis for five years because of end-stage renal failure. The patient complained of right lumbar back pain and fever. Computed tomography and an ultrasonography revealed right hydronephrosis. Pyonephrosis was strongly suspected. A single-J catheter was indwelt, cloudy pus with a terrible smell was discharged. After reducing inflammation, a right nephrectomy was performed. The analysis of stone component revealed mostly a protein calculus, which was a black and turf-like substance in the calices. Patients undergoing dialysis often develop urinary calculi. Some calculi are composed of beta2-microglobulin-origin amyloid, which is very difficult to find with diagnostic imaging.