This paper presents a three-level three-phase diode clamped inverter that uses an auxiliary circuit to equalize its DC-bus capacitor voltages. The proposed converter is used in an Active Power Filter (APF) and a controller is designed for this new APF. A state space model of this filter is obtained first. Three single input single output (SISO) robust controllers are designed to compensate the load current harmonics, to regulate the DC-bus voltage and to equalize the capacitor voltages. The effectiveness of this control strategy is guaranteed by the fact that each of the SISO controllers is provided with appropriate nonlinear terms that compensate the interactions among the filter sub-modules. The APF performance is evaluated. The results demonstrate that load current harmonics are very well compensated, the converter DC-bus voltage is maintained at its reference value and capacitor voltages remain equal despite load variations.