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The work studies to apply a novel FPGA (Field Programmable Gate Arrays) technology to realize a motion control IC for wafer-handling robot which has three-DOF (Degree of freedom) and each axis is driven by PMSM (Permanent Magnet Synchronous Motor). The motion control IC proposed in this paper has two modules. The first module is a Nios II processor which is used to realize the motion trajectory computation and three-axis position/speed controller for the wafer-handling robot. The program developed in Nios II processor uses C language. The second module is presented to implement three-axis current vector controllers by hardware, and the VHDL (VHSIC Hardware Description Language) is applied to describe the controller behavior. Main current vector controller includes PI controller circuit, coordinate transformation circuit, SVPWM (Space Vector Pulse Width Modulation), current comparator circuit, encoder comparator circuit and decode, etc. Therefore, a fully digital motion controller for wafer-handling robot, such as three current vector controllers, three position/speed controller and one trajectory planning, are all implemented by a single FPGA chip. Finally, an experimental system constructed by an FPGA experimental board, one three-DOF wafer-handling robot, one peripheral circuit and three inverters is set up to demonstrate the correctness and effectiveness of the proposed FPGA-based motion control IC of wafer-handling robot.