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This work presents a general filtering and unbalance compensation scheme for electric traction systems. The proposed method uses an active filter controlled with the instantaneous active and reactive power, to reduce the harmonic current distortion and the negative sequence obtained by the system under unbalanced operation in steady state. The proposed filter is evaluated using open delta (V-V) and Scott transformers in the power substation. The scheme has been simulated and experimentally validated. Experimental and simulation results show the controller advantages and the applicability of the proposed method in railway systems.