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Embedded systems present significant security challenges due to their limited resources and power constraints. This paper focuses on the issues of building secure embedded systems on reconfigurable hardware and proposes a security architecture for embedded systems (SAFES). SAFES leverages the capabilities of reconfigurable hardware to provide efficient and flexible architectural support for security standards and defenses against a range of hardware attacks. The SAFES architecture is based on three main ideas: (1) reconfigurable security primitives; (2) reconfigurable hardware monitors; and (3) a hierarchy of security controllers at the primitive, system and executive level. Results are presented for reconfigurable AES and RC6 security primitives and highlight the value of such an architecture. This paper also emphasizes that reconfigurable hardware is not just a technology for hardware accelerators dedicated to security primitives as has been focused on by most studies but a real solution to provide high-security and high-performance for a system.