Although the "gold standard" for diagnosis of tuberculous meningitis (TBM) is bacterial isolation of Mycobacterium tuberculosis (M. Tb), there are still several complex issues. Recently, in the diagnosis of TBM, the detection of M. Tb DNA in cerebrospinal fluid (CSF) samples using PCR has been widely performed as more rapid, sensitive, and specific diagnostic method. Based on Taq Man(R) PCR, the authors developed a novel technique of internally controlled quantitative nested real-time (QNRT) PCR assay that provided a prominent improvement in detection sensitivity and quantification. Total 43 CSF samples from 8 serial patients with suspected TBM were analyzed. The CSF samples were collected before and during standard anti-tuberculosis treatments (ATT). The QNRT-PCR assay revealed positive results for 24 out of 43 serial CSF samples (55.8%) collected during the treatment course of ATT. Moreover, the bacterial cell (BC) numbers of M. Tb analyzed by the QNRT-PCR assay decreased gradually, correlating with the improvements of the patient's clinical conditions. Since the QNRT-PCR assay provides the ability to calculate a numerical value for the initial BC numbers of M. Tb in CSF samples, this method is an extremely useful and advanced technique for use in assessing the clinical course of TBM.