Background: Aboriginal and Torres Strait Islander people are disproportionately affected by hepatitis B virus (HBV) infection. A proposed mismatch between standard vaccines and the HBV/C4 sub-genotype prevalent in Aboriginal people in the Northern Territory (NT) may reduce vaccine effectiveness. Aims: To determine HBV prevalence in the NT by Indigenous status and to explore patterns of immunity following implementation of universal vaccination, using a large longitudinal diagnostic dataset. Methods: A retrospective analysis of all available HBV serology results in the NT from 1991 to 2011 was conducted, with HBV prevalence and vaccination status analysed according to adigenous status, age and sex using individuals' patterns of HBsAg, anti-HBs and anti-HBc serology over repeated tests. Results: 100 790 individuals were tested (33.4% Indigenous) between 1991 and 2011 (26.1% of the 2011 NT population), with a total of 211 802 tests performed. In 2011, the proportion of HBV positive individuals in the NT was 3.17% (5.22% in Indigenous populations) compared to previous 2011 estimates of 1.70% (3.70% in Indigenous populations). The vaccine failure rate was lower than expected with only one presumed vaccinated person subsequently developing HBsAg positivity (0.02%). Evidence of suboptimal vaccine efficacy by breakthrough anti-HBc positivity in vaccinated individuals was demonstrated in 3.1% of the vaccinated cohort, of which 86.4% identified as Indigenous (HR 1.17). No difference in HBeAg positivity or seroconversion was observed between Indigenous and non-Indigenous individuals living with CHB. Conclusions: The burden of CHB in Indigenous people in the NT has previously been underestimated. A higher HBV prevalence in the NT than described in previous cross-sectional studies was found, including a higher prevalence in Indigenous people. Evidence of suboptimal vaccine efficacy was demonstrated predominantly in Indigenous individuals.