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Q fever is a worldwide zoonotic disease caused by the pathogen Coxiella (C.) burnetii. A wide range of animal species is susceptible to this intracellular bacterium with great importance in ruminants. Human infections occur mainly by airborne transmission. C burnetii was detected in animal products such as raw milk, raw-milk cheese and butter prepared from raw milk as well as in the meat of infected animals. In cattle milk, the pathogen was detected up to 13 months after calving. The risk of human foodborne C. Burnetii infection is still considered to be low, but cannot be completely ruled out and remains under discussion. The aim of this study was to compare different laboratory diagnostic methods for C. burnetii in milk sample. The bulk tank and individual milk samples were sent and studied at the National Reference Laboratory for Q-fever in the context of confirmatory laboratory testing after clinical suspicion or retesting of previously antibody detection was in the analysis of 888 individual milk samples a match of 93.3% (Cohen-kappa). A total of 173 bulk milk samples and 2,807 individual milk samples from bovine herds for the presence of C. burnetii DNA and antibodies were tested against the pathogen. The pathogen was detected in 62.5% of the bulk milk samples and up to 60% in individual milk samples. The highest proportion of positive bulk milks was determined as 68.3% in 2012. In individual milk samples, the highest proportion of seropositive samples was 62.2%.