To improve the diagnosis of systemic meningococcal disease we used a nested polymerase chain reaction (nPCR) test to detect meningococcal DNA in cerebrospinal fluid (CSF) samples from patients. The nPCR test was based on the gene coding for the PorA outer membrane protein, a major antigen of Neisseria meningitidis, which is the basis for determining the subtype of the strains. The method was tested on CSF samples from 87 patients with various disease aetiology, including 37 patients with systemic meningococcal disease. It was also applied to all 67 CSF samples from culture-negative patients with suspected meningococcal disease which were collected in the course of the Norwegian serogroup B vaccination trials, between 1987 and 1993. Of the 67 culture-negative CSF samples, 10 were nPCR positive. Two of the 67 CSF were positive with the antigen test, and both of these were nPCR positive. Serum pairs from 46 of the 67 culture-negative patients were analysed for serological serogroup response in an enzyme-linked immunosorbent assay (ELISA) against meningococcal capsular polysaccharides. Nine of the 10 nPCR-positive CSF samples belonged to patients with serological response judged as either typical of, or compatible with systemic meningococcal disease. Sequence analysis of the nPCR products was performed to determine the subtype of the infecting meningococcal strains. Four of the 10 positive CSF samples were infected with a strain of subtype P1.7,16, which is similar to the epidemic strain used to produce the vaccine. Inclusion of nPCR for diagnosis of meningococcal meningitis did not significantly alter the results of the vaccination trial, but added important information about the strain causing disease in 5 of 13 serogroup B cases without preserved isolates.