A PCR system that amplify a repetitive fragment of the insertion sequence IS6110 specific for M. tuberculosis was compared to direct examination in samples from HIV+ and HIV-patients. 138 clinical samples (90 sputa, 30 blood and 18 urines) were analyzed in Senegal, a tuberculosis and HIV endemic area. All smear positive samples were PCR positive except for 7/138 (5.07%) that were false negative because of the presence of inhibitors. However, the use of several samples for each patient minimize the false negative results. The PCR allowed the detection of more positive results in smear negative sputa from HIV- (50%) than in HIV+ patients (20.5%). In contrast, in smear negative blood samples, PCR was positive more frequently in HIV+ (30%) than in HIV- patients (12.5%). Regarding patients, 15/25 HIV+ and 13/17 HIV-patients had at least one positive sample with PCR whereas only 7/25 and 11/17 respectively for HIV+ and HIV- patients had smear positive samples. Thus with some technical cares, PCR might be a useful tool for rapid diagnosis of M. tuberculosis infection in smear negative samples particularly in HIV+ patients.