Despite the diversity of video compression standard, the motion estimation still remains a key process which is used in most of them. Moreover, the required coding performances (bit-rate, PSNR, image spatial resolution,etc.) depend obviously of the application, the environment and the network communication. The motion estimation can therefore be adapted to fit with these performances. Meanwhile, the real time encoding is required in many applications. To reach this goal, we propose in this paper a flexible hardware implementation of the motion estimator which enables the integer motion search algorithms to be modified and the fractional search as well as variable block size to be selected and adjusted. Hence, this novel architecture, especially designed for FPGA targets, proposes high-speed processing for a configuration which supports the variable size blocks and quarter-pel refinement, as described in H.264. The proposed low-cost architecture based on Virtex 6 FPGA can process integer motion estimation on 1080 HD video streams, respectively, at 13 fps using full search strategy (108k Macroblocks/s) and up to 223 fps using diamond search (1.8M Macroblocks/s). Moreover subpel refinement in quarter-pel mode is performed at 232k Macroblocks/s.