In this thesis we describe a new generic approach for accelerating software functions using a reconfigurable device connected through a high-speed link to a general purpose system. In order for our solution to be generic, as opposed to related ISA extension approaches, we insert system calls into the original program to control the reconfigurable accelerator using a compiler plug-in. We define specific mechanisms for the communication between the reconfigurable device, the host general purpose processor and the main memory. The reconfigurable device is controlled by the host through system calls provided by the device driver, and initiates communication by raising interrupts; it further has direct accesses to the main memory (DMA) operating in the virtual address space. To do so, the reconfigurable device supports address translation, while the driver serves the device interrupts, ensures that shared data in the host-cache remain coherent, and handles memory protection and paging. The system is implemented using a machine which provides a HyperTransport bus connecting a Xilinx Virtex4-100 FPGA to the host. We evaluate alternative design choices of our proposal using an AES application and accelerating its most computationally intensive function. Our experimental results show that our solution is up to 5X faster than software and achieves a processing throughput equal to the theoretical maximum.