A difference based current transformer (CT) saturation detection algorithm uses the third difference of a secondary current to detect the instants of the beginning/end of saturation. The third difference of a secondary current contains high frequency components when a CT is saturated. Thus, an effect of an anti-aliasing lowpass filter implemented in digital protection relays on the detection algorithm should be studied. This paper describes performance analysis of a lowpass filter on the CT saturation detection algorithm. The cutoff frequency of the lowpass filter is normally set to be half of a sampling frequency. In this Paper, two sampling frequencies of 3,840 (Hz) corresponding to 64 sample/cycle (s/c) and 1,920 (Hz) corresponding to 32 (s/c) are studied; the cutoff frequencies of the lowpass filters are set to be 1,920 (Hz), 960 (Hz) and 960(Hz), 480(Hz), respectively. And the proposed algorithm is verified by experiment. A 2nd order Butterworth filter is designed as a lowpass filter. The test results and experiment results clearly indicate that the saturation detection algorithm successfully detects the instants of the beginning/end of saturation even though a secondary current is filtered by the designed lowpass filters.