Background Although half of the HIV notifications among Aboriginal and Torres Strait Islander people (‘Indigenous Australians’) are attributed to homosexual transmission, there has been little research examining sexual and drug use risk practices among Indigenous Australian men who have sex with men (MSM). Methods: Respondents were Indigenous Australian (n = 1278) and Anglo-Australian men (n = 24 002) participating in the routine cross-sectional Gay Community Periodic Surveys conducted in Australia from 2007 to 2011. Sociodemographic characteristics, sexual risk practices, drug use, HIV testing and HIV status of Indigenous and Anglo-Australian men were compared and evaluated to discover whether Indigenous status was independently associated with HIV risk practices. Results: Although an equivalent proportion of Indigenous and Anglo-Australian men reported being HIV-positive (9.6%), Indigenous MSM were more likely to report unprotected anal intercourse with casual partners in the previous 6 months (27.9% v. 21.5%; Adjusted odds ratio (AOR) = 1.29, 95% confidence interval (CI): 1.11–1.49). Indigenous men were more likely than Anglo-Australian men to report use of several specific drugs and twice as likely to report injecting drug use in the previous 6 months (8.8% v. 4.5%; AOR = 1.43, 95% CI: 1.11–1.86). Conclusions: Despite a higher proportion of Indigenous men reporting sexual and drug use practices that increase the risk of HIV transmission, there were no differences in the HIV status of Indigenous and Anglo-Australian men. However, the elevated rates of risk practices suggest that Indigenous MSM should remain a focus for HIV prevention, care and support.