In 2009 there were 233 laboratory-confirmed cases of invasive meningococcal disease (IMD) analysed by the National Neisseria Network, Australia, a nationwide network of reference laboratories. One hundred and thirty-five isolates of Neisseria meningitidis from invasive cases of meningococcal disease were available for which the phenotypes (serogroup, serotype and serosub-type) and/or genotype and antibiotic susceptibility were determined. An additional 98 cases were confirmed by non-culture-based methods (92 by nucleic acid amplification testing (NAAT) and six by serology) , and where possible serotyping was determined. Nationally, 194 (83%) laboratory-confirmed cases where a serogroup was determined were infected with serogroup B and 13 (5.6%) serogroup C meningococci. The national total of confirmed cases has remained relatively stable since 2006, but the number of cases may vary between jurisdictions each year. New South Wales had the highest number of recorded cases in 2009. Typical primary and secondary disease peaks were observed in those aged 4 years or less and in adolescents and young adults respectively. Serogroup B cases predominated in all age groups and jurisdictions. The common phenotypes circulating in Australia continue to be B:15:P1.7 and B:4:P1.4. Although serogroup C cases were low, phenotype C:2a:P1.5 again predominated in this group. No evidence of meningococcal capsular 'switching' was detected. Approximately two-thirds of all isolates showed decreased susceptibility to the penicillin group of antibiotics (MIC 0.06 to 0.5 mg/L). All isolates remained susceptible to ceftriaxone. Four isolates had reduced susceptibility to ciprofloxacin, and none to rifampicin.