Anti-tuberculosis drug resistance, particularly multiresistance, is a crucial issue in the control of tuberculosis (TB). This study estimated the prevalence of primary and acquired anti-tuberculosis drug resistance in strains of Mycobacterium tuberculosis isolated from hospitalized patients, to identify the risk factors for resistance, and to evaluate the its impact on hospital mortality for tuberculosis. Strains of Mycobacterium tuberculosis from 217 patients hospitalized for TB were analyzed. Subjects were recruited sequentially at a TB reference hospital in Salvador, Bahia, Brazil from July 2001 to July 2003. Multiresistant (MR) strains were defined as strains resistant to rifampicin and isoniazid. Of a total of 217 strains isolated, 41 (19.0%, 95%CI: 14.1-24.5%) were resistant to at least one drug. Prevalence of primary resistance was 7.0% (10/145), while a prevalence of 43.1% (31/72) was found for acquired resistance. Primary resistance to one drug alone was found in 2.1% (3/145) and acquired monoresistance in 5.6% (4/72). Prevalence of MR strains in general was 14.3% (31/217), of which 4.2% (6/145) consisted of primary MR and 34.7% (25/72) of acquired MR. Three strains showed resistance to more than one drug, but were not classified as MR. In the multivariate analysis, abandoning treatment remained strongly associated with resistance (adjusted OR: 7.21; 95%CI: 3.27-15.90; p<0.001) following adjustment for 3 potential confounders (gender, alcohol dependence and HIV-infection). An association was found between resistance and mortality from tuberculosis, even after adjustment for HIV status, age, sex and alcohol dependence (adjusted OR: 7.13; 95%CI: 2.25-22.57; p<0.001). High prevalences of resistance, principally acquired resistance including MR, were found in patients hospitalized for TB in Bahia. This finding was strongly associated with having abandoned treatment, and confirmed the need to standardize the procedure for requesting sensitivity tests in this population at the time of hospital admission.