Background: Acute rheumatic fever, leading to rheumatic heart disease (RHD), is rare in Australia except amongst Aboriginal and Torres Strait Islander people. Methods: Cardiac surgical procedures performed at Flinders Medical Centre on patients from the Top End of the Northern Territory from 1993 to 2008 were reviewed. This study compared Indigenous and non-Indigenous patients on short term morbidity and long term survival employing logistic regression and Cox proportional hazard models. We also outline the challenges of managing Aboriginal patients, as our unit services vast areas of northern Australia inhabited by Indigenous people. Results: The total number of patients from the Northern Territory was 835. Amongst the Indigenous patients, there were 235 (55.6%) isolated coronary artery bypass graft procedures, 171 (40.4%) patients underwent isolated valvular surgery (91 mitral and 80 aortic), and 17 (4.0%) underwent combined valvular surgery with coronary artery bypass graft surgery. Conclusions: Aboriginal patients requiring valve surgery are younger and have greater comorbidity than non-Aboriginal people. Short term surgical results are similar to non-Aboriginal people but long term outcomes appear to be inferior.Age and socioeconomic conditions of Indigenous patients need to be considered. Cultural issues should be understood and acknowledged and surgery better focused around surgical units with appropriate infrastructure.