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This paper describes the protocol, architecture, and implementation details of an FPGA-based embedded system that is able to remotely reconfigure the FPGA, using a TCP/IP connection, in a secure way. When considering the security aspects, we imply data confidentiality, explicit key authentication and data origin authentication. Since these aspects are overhead for the main application, the system is to be as small as possible. Therefore we have focused on compactness rather than on speed for the implementation. The implemented solution exists out of 2 components: a communication part and a cryptographic part. The system can be easily integrated at any point in the design of an FPGA-based embedded system, due to the simple and modular architecture.