Multichannel MCG noninvasively measures cardiac magnetic field strength from many sites at the body surface, potentially providing useful regional information about ventricular repolarization. Previous work on ECGs has shown that automatic techniques for repolarization measurement are better than manual measurement at discriminating patients with cardiac conditions from normal subjects. Although automatic repolarization measurement techniques have been quantified for ECGs, no comparative data exists for the MCG. In this study four different automatic repolarization (QT) interval techniques for detecting T wave end in the MCG were compared. The influence of MCG filtering on the automatic algorithms was also quantified. MCGs were obtained at 49 sites over the heart from 23 normal subjects. Automatic measurements of the repolarization (QT) interval were made following the addition of different high pass (0.25, 0.5, 1 Hz) and low pass (100, 60, 40, 30 Hz) filters. There were consistent differences between automatic techniques in the unfiltered data amounting to greatest mean difference of 52.3 ms. Low pass filtering significantly increased the automatic repolarization (QT) interval relative to unfiltered measurement by 6.5 (3.2) ms (mean SD) for 100 Hz, 6.0 (3.0) ms for 60 Hz, 8.1 (3.2) ms for 40 Hz, and 8.8 (3.1) ms for 30 Hz across all techniques. High pass filtering significantly decreased the value by -2.6 (6.0) ms for 0.25 Hz, -5.5 (5.3) ms for 0.5 Hz, and -17.1 (7.8) ms for 1 Hz. Automatic measurements of repolarization (QT) in the MCG differ between techniques and are influenced by filtering. These effects should be considered when comparing results.