In Australia, disease registers for acute rheumatic fever (ARF) and rheumatic heart disease (RHD) were previously established to facilitate disease surveillance and control, yet little is known about the extent of case-ascertainment. We compared ARF/RHD case ascertainment based on Australian ARF/RHD register records with administrative hospital data from the Northern Territory (NT), South Australia (SA), Queensland (QLD) and Western Australia (WA) for cases 3-59 years of age. Agreement across data sources was compared for persons with an ARF episode or first-ever RHD diagnosis. ARF/RHD registers from the different jurisdictions were missing 26% of Indigenous hospitalised ARF/RHD cases overall (ranging 17-40% by jurisdiction) and 10% of non-Indigenous hospitalised ARF/RHD cases (3-28%). The proportion of hospitalised RHD cases (36%) was half the proportion of hospitalised ARF cases (70%) notified to the ARF/RHD registers. The registers were found to capture few RHD cases in metropolitan areas (SA Metro: 13%, QLD Metro: 35%, WA Metro: 14%). Indigenous status, older age, comorbidities, drug/alcohol abuse and disease severity were predictors of cases appearing in the hospital data only ( p < 0.05); sex was not a determinant. This analysis confirms that there are biases associated with the epidemiological analysis of single sources of case ascertainment for ARF/RHD using Australian data.