Clostridium perfringens is responsible for Necrotic enteritis (NE) that has been economically important for poultry industry due to the costs of antimicrobial prophylaxis and ineffective feed conversion. Alpha and NetB toxin beside their functions as virulent factor could be major targets for protections and immunity of host against C. perfringens. Various stages of this study was categorized:retrieve sequence of proteinaceous toxins predicting tertiary structure of alpha and NetB toxin, energy minimization, validations of models by Ramachandran plot, conformational and Linear B cell epitope prediction by several different approaches, and finally mapping consensus discontinuous immunogenic regions. Ramachandran plot showed high accuracy of models prediction. By using the combination of B cells epitope predictors for alpha and NetB toxins, 7 and 6 regions (fragments) with immunogenic properties based on consensus agreements on immunogenic residues introduced in different predictor tools in length between 13-30 and 6-34 residues were selected, respectively. Ideally, results of this study helps to interpretation and understanding of the antigen-antibody interactions on a molecular level against these toxins. Moreover designing effective and safe vaccines and producing of monoclonal antibodies for immunodiagnostics methods is another possibly outcome.