The 2009 H1N1 influenza pandemic (influenza A(H1N1)pdm09) disproportionately impacted Indigenous peoples. Indigenous Australians are also affected by a health gap in chronic disease prevalence. We hypothesised that the disparity in influenza incidence and severity was accounted for by higher chronic disease prevalence. We analysed influenza data from Western Australia, South Australia, the Northern Territory, and Queensland. We calculated population prevalence of chronic diseases in Indigenous and non-Indigenous Australian populations using nationally-collected health survey data. We compared influenza case notifications, hospitalisations, intensive care admissions, and deaths reported amongst the total population of Indigenous and non-Indigenous Australians ≥ 15 years. We accessed age-specific influenza data reported to the Australian Department of Health during the 2009 ‘swine flu’ pandemic, stratified by Indigenous status and the presence of one of five chron