The nucleic acid amplification test (NAAT) has been valuable in the diagnosis of urinary tuberculosis; however, no studies have attempted to determine the significance of NAAT post treatment. We encountered three patients with urinary tuberculosis who underwent sequential NAAT during antituberculosis chemotherapy and post treatment. All patients were diagnosed as having urinary tuberculosis by positive NAAT and specific renal deformity revealed by imaging. In two of the three patients, positive culture results were obtained and one was negative in standard culture. During antituberculosis chemotherapy, a negative NAAT was obtained from 3 to 5 months after the start of treatment and no positive culture results were obtained during the same period. At the end of chemotherapy, 6 months or more after the start of medication, all patients had negative NAAT results. These results suggest that NAAT for Mycobacterium tuberculosis provides an effective and rapid detection method for urinary tuberculosis both pre- and post-treatment.