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A novel algorithm based on the correlation analysis of waveforms to distinguish between the magnetizing inrush and the short-circuit fault current is proposed. The algorithm makes use of the characteristics of differential current waveform in the nonsaturation zone that it is similar to a part of the sinusoidal wave under the short-circuit fault and far different with the sinusoid under the inrush condition. To realize this algorithm, the nonsaturation zone of the transformer is decided by comparing the algebraic sum of sampling data in a short slide window of the differential current under the magnetizing inrush or the short-circuit fault, then two kinds of normal sinusoidal waveforms are structured according to the value and position of the peak point of differential current in the nonsaturation zone. The correlation coefficients between the original waveform and two structured sinusoidal waveforms are calculated, and the magnetizing inrush or fault current is judged according to the average of two correlation coefficients. The experimental results verify that the algorithm can correctly open the differential protection shortly for the internal short-circuit fault in operation, energized with a turn-to-turn short-circuit fault, reliably blocking the protection during the magnetizing inrush, and obtaining good immunity to the saturation of the current transformer. Low computation and requirements contributing to this algorithm are performed in practice.