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A nation-wide vaccination campaign began in New Zealand in 2004 with the aim of stopping the epidemic of meningococcal B disease. Approximately 80% of those under 20 years of age when the campaign was launched were vaccinated with three doses of a tailor-made vaccine. We propose a framework for a mathematical model based on the susceptible–carrier–infectious–removed (SCIR) structure. We show how the model could be used to calculate the predicted yearly incidence of infection in the absence of vaccination, and compare this to the effect that vaccination had on the course of the epidemic. Our model shows that vaccination led to a considerable decrease in the incidence of infection compared to what would have been seen otherwise. We then use our model to explore the potential effect of alternative vaccination schemes, and show that the one that was implemented was the best of all the possibilities we consider.