ObjectiveIn Australia, accurate case ascertainment of acute rheumatic fever (ARF) and rheumatic heart disease (RHD) diagnoses for disease surveillance and control purposes requires the use of multiple data sources, including RHD registers and hospitalisation records. Despite drawing on multiple data sources, the true burden of ARF/RHD is likely to be underestimated.MethodsThis study used capture-recapture methods to quantify the missing number of ARF/RHD cases in data from hospitals and jurisdictional RHD registers. Linked datasets comprised reported cases of ARF/RHD in register records and administrative hospital data.ResultsCapture-recapture analyses indicated the total number of new ARF/RHD cases in three Australian jurisdictions (Queensland, South Australia and Western Australia), among people aged 3-54years, was 3480 (95% CI=3366-3600) during 2011-2016. This included 894 (25.7%) individuals who were not listed in either the hospital or register datasets. Non-Indigenous, urban and older people with ARF/RHD were least likely to be identified in either the hospital or register data sources.ConclusionsThe 894 likely ARF/RHD cases our analyses detected that are not included in the routine surveillance datasets are concerning and quantify the magnitude and characteristics of under-notification to RHD registers in Australia, especially for groups that are not typically at high risk of ARF.