Background: There are no contemporary published data on the frequency of the ABO and Rhesus D (RhD) blood groups in the Northern Territory (NT) of Australia, particularly for the large Aboriginal population. Aims: To establish the frequencies of ABO and RhD blood groups in the NT Aboriginal and non-Aboriginal populations in order to aid transfusion inventory management and clinical practice. Methods: Retrospective data were collected from 1 January 2012 to 31 December 2012. All patients with a blood group sample processed by the NT public hospital laboratories and a recorded ABO and RhD report were included. Results were analysed using Stata 14. Results: The Aboriginal and non-Aboriginal populations had significantly different ABO and RhD distributions (P < 0.001). For Aboriginal individuals, 955/1686 (56.6%) were group O and 669/1686 (39.7%) were group A. In non-Aboriginal individuals, 1201/2657 (45.2%) were group O and 986/2657 (37.1%) were group A. We found that 1646/1686 (97.6%) of Aboriginal individuals were RhD positive, compared with 2225/2657 (83.7%) of non-Aboriginal individuals. Only 62/1686 (3.7%) of Aboriginal individuals were group B or AB, compared with 470/2657 (17.7%) of non-Aboriginal individuals. In Aboriginal individuals we found that group O was more common than A in the ‘Northern’ NT, whereas there was similar distribution of the groups in ‘Central Australia’. Conclusions: We found a significant difference in ABO and RhD blood groups between Aboriginal and non-Aboriginal individuals in the NT (P < 0.001). These findings will aid transfusion inventory management, allowing us to plan supply of blood products and reduce waste.