The mechanisms that cause susceptibility to invasive meningococcal disease are largely unknown, but are likely to have important genetic and immunological components. We postulated that susceptibility to meningococcal disease might be associated with altered risks of development of other clinical disease. We studied cancer and immune-mediated disease in people who have been hospitalized with meningococcal disease. In cohorts of people who had invasive meningococcal disease, compared with reference cohorts, the rate ratio for cancer in an Oxford dataset studied from 1963 to 1998 was 0·88 [95% confidence interval (CI) 0·42–1·61] and in an all-England dataset studied from 1999 to 2005 it was 1·02 (95% CI 0·80–1·27). The respective rate ratios for immune-mediated disease were 1·49 (95% CI 0·81–2·50) and 0·69 (95% CI 0·53–0·89). Susceptibility to meningococcal disease was not associated with an altered risk of cancer. Occurrence of immune-mediated disease was, if anything, low in the large all-England cohort of people who had meningococcal disease.