The aim of this study was to describe atypical cerebrospinal fluid (CSF) alterations in tuberculous meningitis (TBM) and to analyse the differences in outcome between patients with typical and atypical profiles. We did a retrospective study during the period of 2000 to 2005 including the cases of TBM assisted in a referral centre for infectious diseases in Rio de Janeiro State, Brazil. Neutrophilic plecytosis at the first spinal tap was found in 32.4% of TBM patients, who had a worse outcome when compared with those patients with typical CSF profiles. One factor that might have a major impact was the delay in starting empirical treatment (27.5 versus 11.6 days). We conclude that, in cases with clinical and epidemiological data compatible with TBM but with an atypical CSF profile, empirical treatment should be considered if CSF culture and direct examination for bacteria are negative.