To identify determinants for mortality and sequelae and to analyse the spatial distribution of meningococcal disease, we linked four national Danish registries. In the period 1974-2007, 5924 cases of meningococcal disease were registered. Our analysis confirms known risk factors for a fatal meningococcal disease outcome, i.e. septicaemia and high age (>50 years). The overall case-fatality rate was 7.6%; two phenotypes were found to be associated with increased risk of death; C:2a:P1.2,5 and B:15:P1.7,16. B:15:P1.7,16 was also associated with excess risk of perceptive hearing loss. The incidence rates of meningococcal disease were comparable between densely and less densely populated areas, but patients living further from a hospital were at significantly higher risk of dying from the infection. To improve control of meningococcal disease, it is important to understand the epidemiology and pathogenicity of virulent successful clones, such as C:2a:P1.2,5 and B:15:P1.7,16, and, eventually, to develop vaccines against serogroup B.