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Background: 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., Methods: 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 chronic conditions: chronic lower respiratory conditions, diabetes mellitus, obesity, renal disease, and cardiac disease. We calculated age-standardised Indigenous: non-Indigenous rate ratios and confidence intervals., Findings: Chronic diseases were more prevalent in Indigenous Australians. Rates of influenza diagnoses were higher in Indigenous Australians and more frequent across all indices of severity. In those with chronic conditions, Indigenous: non-Indigenous influenza notification rate ratios were no lower than in the total population; in many instances they were higher. Rate ratios remained above 1·0 at all levels of severity. However, once infected (reflected in notifications), there was no evidence of a further increase in risk of severe outcomes (hospitalisations, ICU admissions, deaths) amongst Indigenous Australians compared to non-Indigenous Australians with a chronic disease., Interpretation: Higher rates of influenza infection was observed amongst those Indigenous compared to non-Indigenous Australians, and this difference was preserved amongst those with a chronic condition. However, there was no further increase in prevalence of more severe influenza outcomes amongst Indigenous Australians with a chronic condition. This suggests that the prevalence of chronic disease, rather than Indigenous status, affected influenza severity. Other factors may be important, including presence of multiple morbidities, as well as social and cultural determinants of health., (© 2022. The Author(s).)