Clostridium perfringens organisms have an economic concern in poultry production. The purpose of this study was to investigate Net B and β 2 C. perfringens positive isolates in broiler farms and their clinic-pathological effects in broiler chicks. A bacteriological examination of C. perfringens was carried upon 92 Necrotic enteritis (NE) diseased cases and 55 apparently healthy broilers of different ages in Egypt. C. perfringens type A was only recovered (49.7%). cpa gene was detected in 100% of samples with PCR technique. NE diseased cases exhibited both Net B (87.5%) and cpb 2 (75%) toxin genes. Experimentally, an intra-gut induction of Net B and β 2 C. perfringens toxins were evaluated in chicken models. The hematological studies revealed hemolytic anemia 5 days post infection (p.i) in Net B and β 2 inoculated groups (G1&G2). Leucogram revealed neutrophilia and lymphopenia 5 days p.i. A significant increase in ALT, AST, uric acid and creatinine serum levels were recorded in the infected groups at 5 th and 12 th day p.i. DNA Sequencing for net B gene revealed an amino acid replacement from glutamate into arginine at codon 379 with silent mutation was also detected at nucleotide 1134. Sequencing of both toxin genes were recorded in the gene bank for the first time in Egypt. This study pointed out that C. perfringens Net B toxin, is a new key virulent factor for the development of NE. Further studies of Net B toxiod for vaccine production could minimize the clostridial problems in broiler farms.