Food safety has emerged as an important global issue with international trade and public health implications. Bacterial pathogens are major etiological agents of diseases related to the consumption of dairy products and represent a major public health problem in developing countries. Fast and accurate diagnosis of food-borne pathogens using molecular methods such as polymerase chain reaction is very important for a positive outcome of eradication programs. A total of 60 individual raw milk samples were randomly collected from 4 dairy bovine and ovine herds and investigated the presence and the frequency of Listeria monocytogenes, Campylobacter jejuni, Coxiella burntii, Mycobacterium tuberculosis complex and Brucella spp. Overall, 36 (60%) milk samples were positive for the presence of at least one selected food-borne pathogens. The most prevalent pathogen in milk samples was Brucella spp. (53.3%), followed by M. tuberculosis complex (13.3%) and C. burnetii (11.6%). No L. monocytogenes and C. jejuni were detected from any of the milk samples in our study. C. burnetii was detected with slightly higher frequency in bovine samples (8.3%) than in ovine milk samples (3.3%). Moreover, nine (14.9%) bovine milk samples were contained simultaneously more than one pathogen. These evidences reinforce the need to optimize quality programs of dairy products, to intensify the sanitary inspection of these products and the necessity of further studies on the presence of these pathogens in milk and milk products.