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Coxiella burnetii is a zoonotic agent transmitted mainly by small ruminants. In Brazil the disease has been classified as a notifiable disease since 2013, when human cases were reported. This study aimed to identify risk factors associated with the presence of anti- Coxiella burnetii antibodies in goats and sheep in a semiarid region of Northeastern Brazil. Sera of 412 goats and 403 sheep from municipality of Petrolina, Pernambuco, were examined by the Indirect Fluorescent Antibody Test (IFAT) against antigens of C. burnetii. Information about management variables (independent variables) that could be associated with the presence of the microorganism (dependent variables) were obtained from the supervisor of each farm. It was determined that 2.2% (9/412) of the goats and 2.1% (9/403) of the sheep had antibodies reactive to C. burnetii. The presence of anti-C. burnetii antibodies was associated with the dry area of the Sequeiro (a region in the northern part of the municipality of Petrolina) (P = 0.025), male sheep (P = 0.020), and intensive goat breeding (P = 0.005). This study therefore showed the presence of anti-C. burnetii antibodies in goat and sheep, confirming for the first time that this agent is likely circulating among goat herds in the Caatinga Biome, semi-arid of Brazil.