In Victoria, legislation clearly makes the notification of clinical or confirmed cases of meningococcal disease mandatory. Statistical modelling suggests that meningococcal disease is significantly under-notified, and that incorrect codes might be being ascribed to some in-patient episodes. The aims of this study were (i) to test the assumption that cases identified as non-notified cases were true cases, and (ii) to identify the reasons for non-detection on the hospital separation database and non-notification to the infectious diseases unit. Of 26 cases not identified on the in-patient dataset, the main causes were either being given completely incorrect ICD-9-CM codes (11 cases) or being given codes for a different type of meningitis (8 cases). Of 29 non-notified admissions, most were clinically (17) or microbiologically (6) confirmed cases, although 5 were coded in error and were not cases of meningococcal disease. Therefore, although the allocation of incorrect ICD-9-CM codes at separation was a major reason for discrepancy, non-notification was a real and recent problem. It is also possible that some clinical staff did not understand the relationship between Neisseria meningitidis and meningococcal disease, the public health implications of this infection, or the law relating to it.