A total of 755 highly active antiretroviral therapy (HAART)-naive HIV-infected patients were enrolled at a government hospital in Thailand from 1 June 2000 to 15 October 2002. Census date of survival was on 31 October 2004 or the date of HAART initiation. Of 700 (92·6%) patients with complete data, the prevalence of hepatitis B virus (HBV) surface antigen and anti-hepatitis C virus (HCV) antibody positivity was 11·9% and 3·3%, respectively. Eight (9·6%) HBV co-infected patients did not have anti-HBV core antibody (anti-HBcAb). During 1166·7 person-years of observation (pyo), 258 (36·9%) patients died [22·1/100 pyo, 95% confidence interval (CI) 16·7–27·8]. HBV and probably HCV co-infection was associated with a higher mortality with adjusted hazard ratios (aHRs) of 1·81 (95% CI 1·30–2·53) and 1·90 (95% CI 0·98–3·69), respectively. Interestingly, HBV co-infection without anti-HBc Ab was strongly associated with death (aHR 6·34, 95% CI 3·99–10·3). The influence of hepatitis co-infection on the natural history of HAART-naive HIV patients requires greater attention.