Abstract Background Despite large disparities in health outcomes between Aboriginal and non-Aboriginal Australians, detailed evidence on the health and lifestyle characteristics of older Aboriginal Australians is lacking. The aim of this study is to quantify socio-demographic and health risk factors and mental and physical health status among Aboriginal participants from the 45 and Up Study and to compare these with non-Aboriginal participants from the study. Methods The 45 and Up Study is a large-scale study of individuals aged 45 years and older from the general population of New South Wales, Australia responding to a baseline questionnaire distributed from 2006–2008. Odds ratios (OR) and 95% confidence intervals (CI) of self-reported responses from the baseline questionnaire for Aboriginal versus non-Aboriginal participants relating to socio-demographic factors, health risk factors, current and past medical and surgical history, physical disability, functional health limitations and levels of current psychological distress were calculated using unconditional logistic regression, with adjustments for age and sex. Results Overall, 1939 of 266,661 45 and Up Study participants examined in this study identified as Aboriginal and/or Torres Strait Islander (0.7%). Compared to non-Aboriginal participants, Aboriginal participants were significantly more likely to be: younger (mean age 58 versus 63 years); without formal educational qualifications (age- and sex- adjusted OR = 6.2, 95% CI 5.3-7.3); of unemployed (3.7, 2.9-4.6) or disabled (4.6, 3.9-5.3) work status; and with a household income < $20,000/year versus ≥ $70,000/year (5.8, 5.0-6.9). Following additional adjustment for income and education, Aboriginal participants were significantly more likely than non-Aboriginal participants to: be current smokers (2.4, 2.0-2.8), be obese (2.1, 1.8-2.5), have ever been diagnosed with certain medical conditions (especially: diabetes [2.1, 1.8-2.4]; depression [1.6, 1.4-1.8] and stroke [1.8, 1.4-2.3]), have care-giving responsibilities (1.8, 1.5-2.2); have a major physical disability (2.6, 2.2-3.1); have severe physical functional limitation (2.9, 2.4-3.4) and have very high levels of psychological distress (2.4, 2.0-3.0). Conclusions Aboriginal participants from the 45 and Up Study experience greater levels of disadvantage and have greater health needs (including physical disability and psychological distress) compared to non-Aboriginal participants. The study highlights the need to address the social determinants of health in Australia and to provide appropriate mental health services and disability support for older Aboriginal people.