Purpose: To estimate the prevalence of dual diagnosis and identify health, social and criminal justice factors associated with dual diagnosis among incarcerated adults in Australia and Brazil. Methods: We compared data from cross-sectional surveys of incarcerated adults (aged ≥ 18 years) in Australia and Brazil. Using data from linked emergency department, hospital, and in-prison medical records in the Australian sample, and from the Composite International Diagnostic Interview (CIDI) in the Brazilian sample, participants were categorised as having: (1) no mental disorder; (2) substance use disorder only; (3) mental illness only; or (4) dual diagnosis. A multivariate multinomial logistic regression model was fitted to identify factors associated with dual diagnosis in each country. Results: Approximately one quarter of participants in both Australia (22%) and Brazil (25%) met the diagnostic criteria for dual diagnosis. In both countries, dual diagnosis was associated with being female [relative risk (RR) = 2.25 (95% CI 1.47–3.43) Australia; RR = 2.59 (95% CI 1.79–3.74) Brazil], having a history of prior incarceration [RR = 2.99 (95% CI 1.99–4.48) Australia; RR = 2.27 (95% CI 1.57–3.29) Brazil], and having comorbid physical health problems [RR = 1.54 (95% CI 1.08–2.19) Australia; RR = 2.53 (95% CI 1.75–3.65) Brazil]. Conclusions: Despite differences in health, social, and criminal justice systems between Australia and Brazil, the prevalence of and factors associated with dual diagnosis in incarcerated adults appear to be similar in the two countries. A number of generalisable principles can be inferred and should be considered in health and criminal justice policy making.