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The performance of security applications can be greatly improved by accelerating the cryptographic algorithms in hardware. In this paper, an implementation of the secure shell (SSH) application is presented. A self-reconfigurable platform based on a Xilinx Spartan-3 FPGA has been employed to implement a MicroBlaze-based embedded system, which executes SSH under the uCLinux operative system. Run-time reconfiguration is used to change the cryptographic coprocessors utilized for data ciphering. The performance of SSH has been improved and, in comparison to other alternatives not using reconfiguration, a reduction of the area requirements was also achieved.