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In order to improve radar fault diagnosis system, a new architecture of fault diagnosis system based on mobile agents is proposed. The architecture is based on an embedded network built-in radar system. It utilizes all kinds of mobile fault diagnostic agents in embedded network to detect shortcomings of distributed subsystems in radar. In the architecture, all MFDAs can migrate in embedded network, and can be centralized a personal computer so as to be updated and retrained conveniently for different batches of radar systems. In this paper, three kinds of start-up modes of fault diagnosis are illustrated, two kinds of multi-agent cooperation diagnostic frameworks are introduced, and a kind of structure of MFDA is addressed.