Genitourinary tuberculosis (GUTB) is difficult to diagnose in the earlier stage owing to the non-specific symptoms. Usually, renal tuberculous involvement is unilateral and the imaging finding is renal calcification, but associated calcifications of bilateral ureter and bladder are rare. We report a 66-year-old man who presented with diffuse calcification of the urinary system (including bilateral pelvicalyceal system, both ureters and bladder) and disseminated miliary tuberculosis due to GUTB. He had been misdiagnosed with urinary tract infection and urinary lithiasis for two years before the diagnosis of GUTB was confirmed by microbiological examination of the urine. This case highlights the importance of maintaining a high index of clinical suspicion for GUTB.