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This paper analyzes the dc output voltage and line side currents of the three phase PWM boost rectifier under unbalanced and distorted supply voltage conditions. Based on the mathematical model of the three-phase PWM boost rectifier in the positive and negative synchronous rotating frames, a detailed analytical expression for the dc link voltage has been derived and presented. It shows the presence of even order harmonic components in the dc output voltage caused by the negative sequence component of the supply voltages. The effect of the distorted supply voltage on the line side currents has been investigated from the analytical point of view and discussed in this paper. A simple cascaded PI current control scheme in the positive and negative synchronous rotating reference frames has been designed to ensure that the dc link voltage is maintained constant and the supply side power factor is kept close to unity under the unbalanced and distorted supply voltage operating conditions. Experimental test results with the proposed controller are provided on a 1.6 kVA laboratory based PWM rectifier. Test results obtained confirm that the performance of the proposed control scheme enhances the performance of the PWM rectifier over the conventional single reference frame based controller.