Although flies are important vectors of bacterial pathogens, there is little information to assess the health risk of the presence of individual flies especially at animal barns in Sohag Governorate. This study determines the prevalence and the risk of bacterial pathogens associated with the body surfaces of individual wild flies at three different animal barns. A total of 148 caught flies (Musca spp.) were examined and identified into species level. Three fly species (Musca domestica; M. tempestiva and M. sorbens) were detected. Nearly all the collected flies (97.2%) were positive for carrying bacteria. Each positive fly harbored from 1 to 4 isolated bacterial species but most of the flies (61.5%) harbored two species of bacteria. According to the largest variety of bacterial species isolated from these flies, it can be concluded that M. domestica poses the highest risk to the animals and humans, as they are carrying more pathogenic bacteria capable of transmitting many animal diseases, in this particular area. This is followed by M. tempestiva; meanwhile M. sorbens poses the least risk.