A multiplex and duplex PCR procedure was used to identify four toxitypes of Clostridium perfringens collected from apparently healthy and diseased chicken as well as characterization of Clostridium perfringens for the presence of beta2 and enterotoxin genes. Sixty strains of Clostridium perfringens were identified and typed by classical methods. All the strains were analyzed by PCR for the presence alpha, beta, toxin and iota genes as well as beta2 and enterotoxin genes. The results reveal a toxin gene in 45 strains of Clostridium perfringens, only 43 (84.31%) strains of them were identified previously as type A by classical method, as well as 8 strains (15.69%) were identified as type C and 3 strains (5.88%) of type A were associated with beta2 toxin gene by multiplex and duplex PCR typing. Also PCR method can detect 2 other strains of type A directly in the feces and intestinal contents of the examined chicken which gave negative results in traditional examination. Thus PCR technique can become a first-choice tool for the identification, typing and characterization of the virulence genes encoded for enterotoxin and beta 2 of Clostridium perfringens field isolates recovered from poultry which initiate enteric disease in Egypt.