To evaluate the clinical utility of the DNA and RNA amplification assays in monitoring the efficacy of tuberculosis treatment, 416 sputum specimens collected from 15 smear-positive tuberculosis patients during and after treatment were tested for the presence of Mycobacterium tuberculosis by microscopy, culture, polymerase chain reaction (Cobas Amplicor Mycobacterium Tuberculosis Test; Roche, Switzerland) and AMTDT 2 (Amplified Mycobacterium Tuberculosis Direct Test; Gen Probe, USA). All patients were cured, and no relapses were found. Results of both amplification assays re mained positive longer than results of either smear or culture. Four of 15 patients were positive by polymerase chain reaction and/or AMTDT 2 at the completion of treatment. Subsequent sputum specimens from these patients converted to negative within 2.5-12 months. The present data do not support the routine use of qualitative amplification assays for monitoring the treatment response of smear-positive tuberculosis patients.