Abstract: As the fundamental unit of reconfiguring diagnostic system, a new concept, reconfiguring intelligent fault diagnostic agent component group introduced in this paper is utilized to realize diagnostic system reconfiguration. The paper investigates character for diagnosed questions and similarity between them and builds an evaluating way for the intelligent multi-agent diagnostic system with concepts from decision theory. Enlightened by the immune regulation theory in a biotic system, an algorithm for reconfiguring multi-agent diagnosis system is presented in this paper based on general process for reconfiguring intelligent fault diagnostic agent. Physical reconfiguration and logic reconfiguration of AFDS is also illustrated.