With the growth of the portable electronic devices market, not only the protection of the data for the users but also the security of the designs themselves has grown significantly in importance. A solution is presented where a Linux kernel running on a PowerPC processor included in the Virtex-II Pro FPGA family is upgraded to support hardware acceleration on the ciphering tasks. In this way all the programs running on the PPC that make use of the Linux CryptoAPI can be accelerated by hardware in a transparent way without having the programmer to rewrite the applications. To provide more flexibility, the FPGA's self-reconfiguration capability can be used to reprogram any cryptographic algorithm demanded by the Linux CryptoAPI by just including a new software driver for the operating system, thus allowing the internal configuration access port (ICAP) of the FPGA to manage any cryptographic coprocessor at any time. The approach is validated on a real application using the Linux CryptoAPI: a ciphered file system that stores the system data in a secured way.