Coxiella burnetii is a strict fastidious obligate intracellular Gram-negative bacterium, causative agent of an important zoonotic disease called coxillosis or query fever (Q-fever). Due to the dangerous of C. burnetii for human being, the aim of this study is to detect the incidence of such microorganism in farm milk in Assiut governorate in Egypt, by using polymerase chain reaction (PCR). A total of 150 raw milk samples from dairy cattle, ewes and goats (50 samples each) were collected from 5 farms in Assiut governorate, in Egypt. The sampling priority from the animals was upon those having the reproductive problems or mastitis in addition to the presence of ticks which are responsible for transmission of the infection among animals. All the collected milk samples were examined for the incidence of C. burnetii for PCR products of 687 base pairs (IS1111 gene). The obtained results revealed that 9 cattle milk samples (18%), 4 ewes milk samples (8%) and 3 goat milk samples (6%) were positive. In total, 16 out of the 150 milk samples (10.67%) were contaminated with C. burnetii. The revealed results concluded that the raw milk produced in Assiut governorate could be considered a potential source for C. burnetii infection for human being and represented a public health hazard. Consequently, application of food safety management systems and adequate heat treatment of raw milk must be applied to safe the consumer from being infected by coxillosis.