This invention pertains in part to the development of a vaccine for poultry against necrotic enteritis (NE). The vaccine utilizes a protective antigen that is a mutated, full-length, non-toxic Clostridium perfringens (Cp) α-toxin protein (Mcpa). Utility of this vaccine was demonstrated by reduction of lesion severity in NE challenge trails, for example. Also disclosed herein are novel approaches for producing this vaccine in significant quantities. One exemplified approach involves producing NE vaccine (mutated alpha toxin) in bacterial expression systems, preferably utilizing the Pseudomonas fluorescens system, for commercial use in controlling NE in the poultry industry. The subject vaccines can be administered preferably to chickens in several different ways. A novel, Type VI alpha toxin from chicken isolates of Cp is also disclosed.