Introduction: Understanding health inequity is necessary for addressing the disparities in health outcomes in many populations, including the health gap between Indigenous and non-Indigenous Australians. This report investigates the links between Indigenous health outcomes and socioeconomic disadvantage in the Northern Territory of Australia (NT). Methods: Data sources include deaths, public hospital admissions between 2005 and 2007, and Socio-Economic Indexes for Areas from the 2006 Census. Age-sex standardisation, standardised rate ratio, concentration index and Poisson regression model are used for statistical analysis. Results: There was a strong inverse association between socioeconomic status (SES) and both mortality and morbidity rates. Mortality and morbidity rates in the low SES group were approximately twice those in the medium SES group, which were, in turn, 50% higher than those in the high SES group. The gradient was present for most disease categories for both deaths and hospital admissions. Residents in remote and very remote areas experienced higher mortality and hospital morbidity than non-remote areas. Approximately 25-30% of the NT Indigenous health disparity may be explained by socioeconomic disadvantage. Conclusions: Socioeconomic disadvantage is a shared common denominator for the main causes of deaths and principal diagnoses of hospitalisations for the NT population. Closing the gap in health outcomes between Indigenous and non-Indigenous populations will require improving the socioeconomic conditions of Indigenous Australians.