Understanding why carriers of meningococci occasionally develop invasive disease is a major challenge. Individual strains of meningococci are extremely variable and undergo dynamic changes in DNA content and organization. This heterogeneity of meningococcal populations might enhance the fitness of this human-restricted bacterium. The recent discovery of a meningococcal bacteriophage and its associations to disease is an intriguing example of this variability and could contribute to a better understanding of microbial commensal and virulence behaviour.