OBJECTIVE: To evaluate the presence of bacteria in samples from patients suffering from 'aseptic' meningitis following craniotomy. METHODS: Prospective study in which cerebrospinal fluid (CSF) from patients suffering from post-craniotomy meningitis and negative control patients were submitted to conventional culture and to polymerase chain reaction (PCR) using bacterial 16S rRNA universal primers, followed in some cases by DNA sequencing of the PCR product and phylogenetic analysis. RESULTS: CSF from patients with either culture-positive or culture-negative meningitis yielded positive amplifications, whereas no amplification was obtained with CSF from control patients. All positive signals were confirmed by Southern hybridization with a prokaryote 16S RNA-specific probe. Six PCR products, of which three were collected from later cases of culture-negative meningitis, were cloned and sequenced. Sequence analysis suggested affinities with Pseudomonas in three cases, with Escherichia in two cases and with Rhodococcus in one case. CONCLUSIONS: Many cases of culture-negative (aseptic) meningitis are probably bacterial meningitis and justify antibiotic treatment. The bacteria responsible for these cases of culture-negative meningitis might have peculiar growth requirements in vitro.