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The papers in this special section focus on compiler optimization for FPGA-based systems. Reconfigurable computing (RC) is growing in importance in many computing domains and systems, from embedded, mobile to cloud, and high-performance computing. We have witnessed important advancements regarding the programming of RC-based systems, but further improvements are needed, especially regarding efficient techniques for automatic mapping of computations described in high-level languages to the RC resources. The resources of high-end FPGAs allow these devices to implement complex Systemson- a-Chip (SoCs) and substantial computational components of software applications, e.g., when used as hardware accelerators and/or as more energy-efficient computing platforms. This, however, increases the continuous need for efficient compilers targeting FPGAs, and other RC platforms, from high-level programming languages.