In this study, the presence of Coxiella burnetii (Cb) in cheese produced in Southern Italy from milk of cow, buffalo, and small ruminants has been evaluated. Two tests based on real-time PCR assay targeting CB IS1111 element were performed. First an assay based on the use of Taq-Man probe was performed to screen the samples. The positive samples were confirmed using both a SyBr Green test and the evaluation of the melting temperature of the amplicons. In addition, all cheese samples were also tested to determine the milk species utilized (Regulation EC 273/2008). The samples of cheese produced with a milk mix from different species were not included into the study. A total of 169 cheese samples were tested, and the obtained results showed an overall prevalence of Cb of 21.3 % with variation between species. A positivity rate of 39 % was observed in cow's cheese while Cb DNA was detected in 26 % of cheese samples made from small ruminants' milk. However, the bacterium was found only in 6.9 % of buffalo's cheese samples. A direct association between prevalence and milk used for the production was highlighted (chi (2) = 19.12). The statistical analysis of the prevalence in the samples from cattle and small ruminants compared with those from buffalo shows an OR of 8.4 and 4.9, respectively.