This book constitutes the refereed proceedings of the 5th International Workshop on Applied Reconfigurable Computing, ARC 2009, held in Karlsruhe, Germany, in March 2009. The 21 full papers and 21 short papers presented together with the abstracts of 3 keynote lectures were carefully reviewed and selected from about 100 submissions. The papers are organized in topical sections on FPGA security and bitstream analysis, fault tolerant systems, architectures, place and route techniques, cryptography, and resource allocation and scheduling, as well as on applications.