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This paper introduces a novel algorithm for differential protection of three-phase power transformers that is based on the wavelet packet transform. The wavelet packet transform is employed to extract certain features of the differential current to distinguish between the magnetizing inrush and different internal fault currents. The selection of the optimal wavelet analysis that includes selecting both the optimal mother wavelet and the optimal number of levels of resolution is carried out using the minimum description length (MDL) data criteria. The proposed algorithm is tested off-line using data collected from a prototype laboratory three-phase power transformer. The test results show reduced computational burden, high speed and high accuracy.