Clostridium perfringens (C. perfringens) is a Gram-positive anaerobic spore-forming bacterium that is widespread in environmental soil and sewage, as well as in animal intestines. C. perfringens is an important pathogen in both human and veterinary medicine. The incidence and numbers of C. perfringens in the intestinal contents of 100 cattle, 86 turkey and 177 chickens from September 2015 to April 2016 were determined. C. perfringens was found in 26%, 22% and 40% of intestinal contents of cattle, turkey and chickens, respectively. In this research samples were tested for isolation of C. perfringens by culturing and biochemical method and then they were confirmed by the polymerase chain reaction (PCR) methods. We suggest that PCR assay could be a replacement of the culture method for quantifying C. perfringens in the intestinal tracts. These research helping us to establish the role of each C. perfringens toxin in animal disease, to investigate the in vivo mechanism of action of these toxins, and to develop more effective vaccines against diseases produced by these microorganisms.