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The MPEG-4 and H.263 video standards are enabling technologies for the proliferation of wireless multimedia applications in 3G systems. For video encoding, the motion estimation (ME) stage is typically the most demanding in terms of performance and bandwidth requirements, and is usually implemented through dedicated hardware, especially in systems with stringent power requirements. This approach, however, cannot exploit any algorithm advances on motion estimation algorithms, and requires major hardware re-design in case of modified specifications or standards. This paper describes the architecture of a programmable motion estimation unit that is used as part of a larger wireless video encoding system. An instruction set architecture (ISA) allows the development of various ME algorithms in software without the need to re-design portion of the chip.