A review of the epidemiology of meningococcal disease (MD) in Australia was undertaken, with particular emphasis on the 1990s, when national strain differentiation data became available. The data included a review of clinical and laboratory notification data and published reports on clusters and outbreaks. There have been considerable changes in the patterns of MD in the 1990s. In some cases, these changes can be related to the dominance of a particular phenotype. In the early 1990s, widely scattered urban and rural clusters were associated with the phenotype C:2b:P1.2 and strains were closely genetically related. Larger urban clusters and increased numbers of cases in adolescents and young adults were most obvious in New South Wales in the mid-1990s and were associated with a phenotype C:2a:P1.5. This ET-15 clone of the ET-37 complex caused similar patterns of MD to those seen in other countries as part of the global spread of the clone. In contrast, the B:4:P1.4 phenotype, with close genetic similarities to New Zealand strains, did not cause the hyperendemic disease seen in New Zealand this decade. The epidemiology of MD will continue to exhibit considerable variation due, at least in part, to the genetic flexibility of meningococci. Information about strain variation expands our understanding of changing patterns of disease.