Coxiella burnetii is an obligate intracellular bacterium, causing a zoonosis called Q fever. The detection of this etiological agent and its epidemiology in an area is important to estimate the risk of infection. Ruminants are the main source of the infection and sheep are considered very important for the spread of the agent, by birth products, but also vaginal mucus, milk and faeces. Moreover, C. burnetii is considered a food-borne pathogen and the Mediterranean dairy sheep flocks are used to produce dairy food, using occasionally unpasteurized or raw milk. Samples of bulk-tank milk and fecal pools from 15 Umbrian flocks, randomly selected, were analyzed by PCR to detect C. burnetii DNA. The methods of milk treatment were recorded for each farm to define the possible risk for the transmission of infection to humans. Two farms were positive both from bulk-tank milk and fecal pools, while another one only from bulk-tank milk. All samples of the other farms were negative. Considering these results, the estimated prevalence was 20,0% for the bulk-tank milk (Confidence Interval, CI, 95%: 8,6-38,6) and 13,3% for the faeces (CI 95%: 4,3-30,0) of the sampled farms. The results showed that C. burnetii is present in Umbrian dairy sheep flocks and every farm could have a different risk of infection based on milk-processing in farm. Further studies on the infection will be needed to estimate the prevalence of the infection and to define the category of risk for each farm.