Resistant tuberculosis is an important public health problem in South Sulawesi, Indonesia. We conducted a retrospective cohort study of 1,582 smear positive tuberculosis patients registered with the National Tuberculosis Program during 2007 in Makassar, Indonesia, to assess risk factors associated with poor tuberculosis treatment outcomes. Of the 1,582 patients, 265 had a poor treatment outcome. Of the 265 patients with a poor treatment outcome, 216 had defaulted on treatment, 7 failed treatment, 9 died and 33 transferred to another area. After adjusting for sex, age and BCG status, failure acid-fast bacilli (AFB) positive sputum to convert to AFB negative by 2-3 months was the only risk factor significantly associated with a poor treatment outcome (odds ratio 7.57; 95% CI: 1.22-47.1). We hypothesise this could represent resistant tuberculosis. Early identification of resistant tuberculosis is important and should be suspected in patients whose AFB positive sputum samples fail to convert to AFB negative by 2-3 months.