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This paper presents a digital plug-in frequency domain based repetitive control scheme for minimizing the odd order harmonics in the supply line side currents of the three phase pulsewidth modulation (PWM) boost rectifier under the distorted and unbalanced supply voltage conditions. Based on the mathematical model of the three-phase PWM boost rectifier under the generalized supply voltage conditions, the control task is divided into: (a) dc-link voltage harmonics control and (b)supply line side current harmonics control. The proposed plug-in repetitive controller together with the conventional PI controller is designed to achieve supply line side currents with low total harmonic distortion (THD) for the three phase PWM boost rectifier. The repetitive control learning algorithm is implemented in the frequency domain by means of Fourier series approximation, instead of commonly used time domain based scheme, and provides the flexibility of choosing different learning gains and phase angle delay compensations individually for each harmonic component. The experimental test results obtained from a 1.6 kVA laboratory based PWM rectifier confirm that the THD of the supply line side currents can be reduced from 21.09% to 4.12% with the plug-in frequency domain based repetitive current controllers.