A 40-year-old man with intractable meningitis was transferred to our hospital 6 weeks after onset. On admission, he showed consciousness disturbance, meningeal signs and right oculomotor nerve palsy. MRI demonstrated prominent cisternal enhancement and hydrocephalus. We suspected tuberculous meningitis as the diagnosis, and treated with antituberculotics, though he died of midbrain infarction day 11 of the treatment. Before and during the admission, bacterial cultures, PCR, smear examination of cerebrospinal fluid(CSF) were repeated. But no evidence of tuberculosis was obtained. Cultures of the brainstem fragments detected mycobacterium, which was finally confirmed by a PCR method after his death. PCR provides a rapid and reliable diagnosis of tuberculous meningitis, although there is a potential for false-negative. Thus the clinical, radiological and CSF findings should be stressed. Corticosteroids treatment should be considered in cases with ischemic lesions.