In the present study, 6 C.perfringens strains (4 were type A and 2 were type D) were recovered from intestinal and liver samples of 6 diseased broiler. PCR  used for the detection of  alpha and epsilon toxin . Multiplex PCR was done to C.perfringens isolates which had the gene  gave a characteristic` band at 402 bp and 541 bp where all of the 6 isolateswere positive for alpha  toxin genes.The extracted toxins were purified by ammonium sulfate precipitation, then profiling of the exotoxin proteins by sodium dodecyl sulphate polyacrylamide gel electrophoresis  (SDS-PAGE).SDS-PAGE has become an important tool for protein profiling which reflect the genetic identity to C.perfringense type A and D. Our study revealed the histopathological changes of  intestinal  samples of the diseased birds with necrotic enteritis showed Intestine hyaline degeneration of the muscle, fragmentation and edema in between the muscle infiltrated with inflammatory cells. Liver showing fibrous connective tissue in the portal area particularly around intrahepatic bile duct and hyperplastic proliferation of biliary epithelium toward the lumen associated with central vein.