Tuberculose has increased in the recent years. Use of a sensitive screening method, can be one of the influential parameters in reduction of pulmonary tuberculosis. Current screening method in the laboratories is based on observation of bacilli in stained smear by Ziel-Neelsen procedure. The aim of this research was to study the PCR efficiency in all confirmed patients of Hamadan province. Twenty eight patients were registered as having pulmonary tuberculosis by the tuberculosis comity of the Hamadan province. All these patients had positive results for staining and culture. Amonst these registered patients, we could access only to the 12 patients during the study. Sputums were collected from early stage of diagnosis and continued during treatment at the end of each month. All these patients were under the treatment by the DOTs protocols. All samples were tested by PCR and the results were compared with Ziehl-Neelsen staining method that is recommended procedure by WHO. Compared results showed none of the samples were positive by staining method at the end of second month up to the last month of treatment, while PCR changed to negative gradually. It was negative in 5 and 4 patients at the end of the third and forth month, respectively. Specimens of the three remanied patients were continuously positive up to the end of treatment period. Gradually changing PCR results to negative in three forth of studied patients means it can be applicable screening tools, but one forth remained positive cases needs more study for the evaluation of target gene role and efficiency of the test.