We sought to estimate mortality and associated factors in HIV-hepatitis co-infected individuals in Michigan using a retrospective cohort study. For the study period of 1 January 2006 to 31 December 2009, all HIV-infected individuals were matched to hepatitis B and C cases. In the final Cox proportional hazards regression model, individuals of other [hazard ratio (HR) 2·2, 95% confidence interval (CI) 1·4–3·2] and black (HR 1·3, 95% CI 1·1–1·6) race had decreased survival compared to white race. Similarly, injecting drug users (IDUs) (HR 2·1, 95% CI 1·6–2·6), men who have sex with men (MSM)/IDUs (HR 1·5, 95% CI 1·1–2·2), individuals with undetermined risk (HR 1·5, 95% CI 1·2–1·9) and heterosexual practices (HR 1·4, 95% CI 1·1–1·8) had decreased survival compared to MSM. Additionally, an interaction was found between current HIV status and co-infection. Mortality in HIV-hepatitis co-infected individuals remains a continuing problem. Our study can help in planning interventions to reduce mortality in HIV-infected individuals.