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<p>Ruminants are the main reservoir of <em>Coxiella burnetii</em>, an obligate intracellular Gram negative pathogen. This microorganism is the causative agent of Q fever, a a zoonosis transmited to humans by contacting contaminated fluids from infected animals, inhaled aerosols or consuming milk from infected animals. We used Real-Time PCR assay with a Taq-Man fluorescent probe to detect the pathogen in samples of bovine milk collected from random locations in nine Ecuadorian provinces. The assay targeted a 61-63bp repetitive sequence within the IS1111 transposon in <em>C. burnetii</em>. The assay found positive samples in two provinces located close to the Colombian and Peruvian borders and in Chimborazo (Ecuadorian central region). This study is the first in Ecuador to detect <em>Coxiella burnetii</em> using a molecular method of high sensitivity.</p>