In this paper, compression of fpga bit streams has been implemented. Bit stream compression is important in reconfigurable system design since it reduces the bit stream size and the memory requirement. It also improves the communication bandwidth and thereby decreases the reconfiguration time. In this paper, two compression methods are used. Compression of fpga using bitmask based compression and Huffman coding is discussed. Compression of fpga bit streams is obtained. Bitmask based compression method outperforms the Huffman coding method by an average of 15%. The results obtained using these methods is compared. The Bitmask based compression method produces a better compression ratio compared to Huffman coding method.