A seroepidemiological study was conducted on the presence of Coxiella burnetii (C. burnetii) antibodies in sheep and goats in Istria, the largest peninsula in Croatia. Random blood samples were taken from 634 sheep and goats at different localities throughout the region. The aim of the study was to assess the prevalence of C. burnetii infection in sheep and goats, which represent the most important reservoir of infection in humans. C. burnetii antibody detection was performed by ELISA (LSIVet Ruminant Q Fever-Serum/Milk). Seroprevalence of C. burnetii was proven in 6.2% of sheep and 3.5% of goats. Larger herds, poor hygienic conditions on farms, a higher presence of goats in a restricted area, and the northern part of Istria proved to be significant risk factors for the seropositivity of animals.The southern part of Istria is known to have endemic Q fever, but no studies have been carried out so far to explore this issue. To gain a more complete epidemiological picture of Q fever in Istria, studies in humans, especially those professionally exposed to C. burnetii infection, should be performed.