The polymerase chain reaction (PCR) using oligonucleotides based on the repetitive sequence (IS6110) of Mycobacterium tuberculosis and Amplicor Mycobacterium, which combines a PCR with the hybridization assay, were evaluated for detection of M. tuberculosis in pleural fluid and gastric juice. The detection limits of these two assay systems for cultured M. tuberculosis were less than 2 cells/ml, as compared with 200 cells/ml by culture. A total of 42 pleural fluid and 94 gastric juice specimens were examined. A total of 5 pleural fluid and 5 gastric juice were culture positive for M. tuberculosis. Only the PCR gave positive results in 2 pleural fluid of which laboratory findings are characteristic of tuberculous pleuritis, and in one gastric juice of the patient who was diagnosed as having pulmonary tuberculosis. Sensitivity, specificity and positive predictive value for IS6110 gene were 75%, 94% and 71.1%, respectively, in pleural fluid. Two of three positive specimens for IS6110 gene from pleural fluid were negative for Amplicor Mycobacterium. These specimens resulted in positive with Amplicor Mycobacterium when solvent extracted DNA was used. Both the PCR systems had the same sensitivity (80%), specificity (98.8%) and positive predictive value (83.3%) in gastric juice. The PCR systems would be useful for rapid detection of M. tuberculosis without long term culture and for detection of non-cultured one from pleural fluid as well as gastric juice. However, when the presence of an inhibitor of PCR is suspected in a specimen, DNA should be purified from the specimen before amplification.