Neisseria meningitidis poses a major disease burden on human beings. Meningococcal typing has a longstanding tradition for epidemiological surveillance of the disease. Genetic and antigenetic variability resulting from horizontal genetic exchange has been exploited for this purpose. Neisseria meningitidis served as the bacterial prototype organism for the development of multi locus sequence typing, which has replaced multi locus enzyme electrophoresis as the gold standard for meningococcal typing. Due to the rapid emergence of new porin variants serotyping by monoclonal antibodies is currently being replaced by DNA sequencing of variable regions of the porA gene. Sequence data were used to characterize the population structure of meningococci in carriage and disease. The advances in molecular epidemiology of meningococcal disease, and the rapid exchange of DNA sequence data via curated internet websites have resulted in an interactive international network, which is capable of identifying newly emerging clones within weeks.