Monthly clinical and microbiological parameters (by sputum smear, culture and PCR assay), of 50 patients with documented pulmonary tuberculosis and on anti-tuberculosis therapy, were monitored over a period of 18 months. PCR converters (70%) who had PCR conversion before the sixth month of treatment did not have clinical or microbiological evidence of failure or relapse, while nine of 15 PCR persisters (30%) had clinical failure (7) and relapse (2). The PCR persisters were significantly associated with more underlying medical illnesses, high mean radiographic scores on the extent of disease involvement, previous drug treatment, initial sputum smear positivity and multi-drug resistance. Of the eight PCR persisters infected by susceptible Mycobacterium tuberculosis, all had marked residual radiographic changes despite completion of drug therapy. The findings may have important implications in the application of PCR on individualization of the duration of anti-tuberculosis therapy.