A reference hospital for tuberculosis (TB) and human immunodeficiency virus/acquired immune-deficiency syndrome (HIV/AIDS) with a TB control programme in Rio de Janeiro, Brazil. To estimate the prevalence of resistance to anti-tuberculosis drugs and to identify associated factors. In a cross-sectional study, clinical and laboratory data were collected retrospectively from 2001 to 2005. Patients with isolation of Mycobacterium tuberculosis and available drug susceptibility tests were considered eligible. Data on demographic characteristics, risk factors for resistance, HIV serology and past TB history were collected and analysed by chi(2) Mann-Whitney test and Poisson regression. We analysed 350 treatments, of which 62 were for patients with previous TB. HIV status was positive in 31.2% of cases. Resistance was found in 15.7% and multidrug resistance (MDR) in 4.3% of cases. Previous treatment (P < 0.001) and relapse within 2 years were associated with resistance (P < 0.03). Pulmonary cavities were associated with MDR (P < 0.001). Homelessness was associated with any resistance in newly diagnosed patients (P < 0.01). Working in a hospital was not associated with resistance. Suspicion of drug-resistant disease is necessary in patients with a history of previous TB in hospitals in Rio de Janeiro. The implementation of an effective hospital TB control programme can prevent transmission even in high TB prevalence settings.