Objective. The aim of this study was to provide molecular evidence of C. burnetii in sheep and goats from some herds of Valledupar, Cesar, Colombia. Materials and methods. Fifteen herds of sheep and goats were chosen by convenience to investigate the infection by C. burnetii, during March and April of 2013. 328 female goats and 66 sheep from 15 herds were included in this study. Milk from ewes and vaginal mucus samples from goats were analyzed by Polymerase Chain Reaction for DNA detection of transposase gene (IS1111) of C. burnetii. Results. DNA of C. burnetii in 6% (4/66) of sheep's milk and 0.6% (2/328) vaginal mucus from goats was found. 13% (2/15) of the herds had at least one infected animal. Discussion. Our findings suggest the circulation of C. burnetii in sheep and goats from some herds of Valledupar, Colombia, and it highlights the possibility of occurrence of infections in humans and animals. Conclusions. The detection of C. burnetii in sheep milk could represent a public health risk factor for people who consuming raw milk, cheeses or people associated to agriculture and livestock handling. Further studies are necessary to evaluate other routes such as tick's bite, feces, milk from goats and vaginal mucus from sheep of this region of Colombia.