Microbial agents may play a role in the pathogenesis of multiple sclerosis (MS). C. pneumoniae has been recently associated with MS; however, study results are at variance. We tested the hypothesis that Chlamydia pneumoniae-specific DNA and RNA are more often detected in cerebrospinal fluid (CSF) of patients with multiple sclerosis than patients with other neurological diseases (OND). We investigated CSF samples from 84 patients with definite MS and 89 OND patients (n = 62 with normal CSF; n = 27 with pathological CSF) using a nested polymerase chain reaction (PCR) to detect ompA gene sequences of C. pneumoniae. In subjects with positive PCR, we probed for chlamydial heat shock protein 60-mRNA and 16S-rRNA by reverse transcriptase (rt)-PCR.