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ABSTRACT The Mato Grosso do Sul State (MS) has the second-largest indigenous population and the highest incidence rates of TB among indigenous people in Brazil. However, little is known about the risk factors associated with active TB in indigenous people in the region, especially regarding socioeconomic factors. The aim of this study is to assess the effect of the Family Allowance Program (BFP) and of other predictors of active TB in a high-risk indigenous population in Brazil. We conducted a case-control study with incident TB cases matched by age and by village of residence (1:2 proportion) between March 2011 and December 2012. We used a conditional logistic regression for data analysis. A total of 153 cases and 306 controls were enrolled. The final model included the following risk factors: alcohol consumption (low-risk use OR=2.2; 95% CI 1.1-4.3; risky use OR=2.4; 95% CI 1.0-6.0; dependent/ damaging use OR=9.1; 95% CI 2.9-29.1); recent contact with a TB patient (OR=2.0; 95% CI 1.2-3.5); and male sex (OR=1.9; 95% CI 1.1-3.2). BFP participation (OR=0.5; 95% CI 0.3-0.6) and BCG vaccination (OR=0.5; 95% CI 0.3-0.9) were found to be protective factors against TB. Although the BFP was not designed to target TB-affected households specifically, our findings reveal the importance of the BFP in preventing one of the most important infectious diseases among adults in indigenous villages in Brazil. This result is in line with the End-TB strategy, which identifies social protection, poverty alleviation and targeting other determinants of TB as key actions.