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A discrete-time linear control strategy for a multilevel three-phase unified power quality conditioner (UPQC) based on single-phase power cells is presented. The multi-variable, nonlinear, and coupled features of these topologies make the control strategy design a difficult task. Controlling this kind of system with single-variable linear controllers-as proposed in this work-presents significant advantages compared with other approaches as simplicity in the design steps due to the large amount of tools developed for this kind of schemes. Particularly, a classic design method based on the root locus approach is used to choose the controllers parameters in order to achieve a given dynamical behavior. Compensation of reactive power and fundamental frequency disturbances is presented in this paper as part of a general control strategy for multilevel active power filters. The proposed control strategy is implemented on the TMS320C6713 DSP-based system for a low-power laboratory prototype, and thus the controllers design is carried out on the discrete-time and -frequency domain. Also, due to the inherent asymmetries among the power cells in a modular topology, a dedicated local control strategy is proposed to ensure a symmetrical distribution of the power among the power cells. This feature allows the semiconductor devices of each module to operate under the same voltage and current ratings. Simulated and experimental results showing stationary and transient conditions demonstrate the feasibility of the control scheme.