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Recent advances in device densities and the requirement for short time-to-market has made FPGA devices very popular for the implementation of general purpose electronic devices. Modern FPGA architectures offer the advantage of partial reconfiguration, which allows an algorithm to be partially mapped into a small and fixed FPGA device that can be reconfigured at run time, as the mapped application changes its requirements. Such a feature can be beneficial for modern control applications, that may require the change of coefficients, models and control laws with respect to external conditions. This paper presents an embedded run-time reconflgurable architecture for the design of a fuzzy logic PID controller. The proposed solution is both technically advanced and cost effective, offering flexibility, modularity and efficiency, without performance reduction.