Q fever is a disease of high zoonotic potential, but interest in its causative agent is rather low although it causes some public health problems in Hungary. The prevalence of Q fever is highly variable by country. The main reservoirs of the disease are the same domestic ruminant species everywhere, but the epidemiological profile depends on the features of the specific reservoir. The aim of this large-scale study was to demonstrate the importance of Q fever in different species as a possible source for human infection in most regions of Hungary. A total of 851 serum samples from 44 dairy farms, 16 sheep flocks, 4 goat farms and 3 zoos located in different parts of Hungary were tested. The presence of antibodies to Coxiella burnetii was surveyed in dairy cattle (n = 547), goats (n = 71), sheep (n = 200) and zoo animals (n = 33). The animal species tested in Hungary showed different seroprevalence values of C. burnetii infection. Seropositivity by the enzyme-linked immunosorbent assay was found in 258 out of 547 (47.2%) cows and in 69 out of 271 (25.5%) small ruminants, among them in 47 out of 200 (23.5%) sheep and in 22 out of 71 (31.0%) goats. Antibodies to C. burnetii were not detected in zoo animals. Seropositivity was demonstrated in 44 out of 44 (100%) dairy cattle farms, with at least one serum sample found to be positive on each farm. The seropositivity rate of small ruminant farms was 55.0% (11 positive out of 20 tested), with 9 out of 16 (56.3%) sheep flocks and 2 out of 4 (50.0%) goat herds showing seropositivity.