The prognosis of tuberculous meningitis (TBM) depends on early therapy based on rapid diagnosis. To study the clinical value of PCR in diagnosis of TBM, we investigated CSF specimens from 49 patients. After cell lysis and DNA preparation following a standard protocol, we performed a half-nested PCR with primers able to detect mycobacterial DNA. PCR results were evaluated according to clinical features, histopathological data, and bacteriological results. PCR detected four of five cases of confirmed TBM, corresponding to a sensitivity of 80%. Positive PCRs were also obtained in 25% CSF samples of non-TBM patients. Most of these false positive results were due to amplification of Mycobacteria fortuitum (M. fortuitum) as determined by direct sequencing analysis. To enhance specificity of our half nested protocol, the oligonucleotide primers that were specific for several mycobacterial subspecies were substituted by a primerpair, which allows selective amplification of DNA from Mycobacteria tuberculosis (M. tuberculosis). By using the altered PCR protocol, the screening of CSF samples revealed a much higher specificity (97%) and constant sensitivity (80%) in diagnosis of TBM. These findings indicate, that M. fortuitum, as an ubiquitous mycobacterial subtype of low pathogenicity, can potentially contaminate clinical specimens and account for false positive PCR results. Therefore, the clinical value of PCR in diagnosis of TBM strongly depends on appropriate oligonucleotide primers, that allow to differentiate between mycobacterial subtypes.