The antigenic characteristics of the class 3 outer membrane protein of Neisseria meningitidis has been important both in the identification of outbreak strains and for the development of OMP vaccines. Current serotyping methods do not characterize all antigenic regions and many disease isolates are serologically non-typeable. Four major variable regions (VR) in the class 3 OMP gene (porB) encode surface exposed antigenic regions of the protein. We have developed a panel of oligonucleotide probes to each porB VR of the 10 class 3 expressing serotype strains and one probe to a conserved region of class 2 porB. Using PCR amplification of porB with subsequent hybridization of the PCR products, we have obtained both diagnosis and typing information directly from a series of culture positive and culture negative CSF samples from Brazil. This method expanded the available data by providing genotype information for cases that were culture positive but serologically non-typeable and cases that were clinically diagnosed as meningococcal meningitis but were culture negative. The epidemiology of individual variable region genotypes shown by this method may be of importance in vaccine development.