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This paper deals with the problem of the design of an all-digital implementation of a three-phase PLL and the control logic of a shunt active filter implemented with a Multilevel Current Source Inverter (MCSI). The active filter is connected to the medium voltage level of a power distribution system where compensation of reactive power and harmonics is mandatory. The PLL is essential to obtain a reference frame for grid synchronization. The performance of proposed PLL structure and logic control is simulated via Matlab/Simulink. The proposed PLL structure shows fast synchronization and adequate tolerance to grid voltage unbalance. Both the PLL and the control logic can be downloaded and tested on a Field-Programmable-Gate-Array (FPGA) using the same software tool.