This paper describes a novel FPGA (Field Programmable Gate Array) based control system for MSAF (Motor Side Active Filter). The MSAF is based on the active filtering approach and its main task is to obtain an optimized power sharing between two Voltage Sources Inverters (VSIs). This solution allows to obtain an optimal VSI parallel connection both reducing the total switching losses and, in the same time, improving the quality of the motor currents. In this paper particular attention is paid to the implementation of a high performance FPGA based current controller (500kHz). Simulated and experimental results are given and discusses.