Multichannel magnetocardiography (MCG) noninvasively measures variations in magnetic field strength from many sites at the body surface, potentially providing useful regional information about ventricular repolarization. MCGs contain features similar to ECGs, and although errors associated with repolarization measurement have been quantified for ECGs, no comparative data exists for MCGs. In this study, errors in manual measurement of repolarization interval in the MCG were determined. Sixteen MCG channels and three ECG leads were recorded simultaneously in eight healthy subjects. Each recording was displayed in a random order on a computer screen, in presentations with different noise levels, time display widths, and amplitude display heights. In total, manual measurement of repolarization intervals in 2,048 (eight subjects x 16 channels x eight presentations x two repeats) MCGs were made by each of four analysts. Measured repolarization intervals were reduced by 3 ms when noise was added and by a further 3 ms when this noise was doubled. Intervals were shortened by 9 ms when the time display width was doubled and by a further 10 ms when the display width was doubled again. Measurements increased by 7 ms for a doubling of amplitude display height, equivalent to a doubling of T wave height. There were also consistent differences between analysts; amounting to a greatest mean difference of 24 ms. Display characteristics, added noise, and different analysts thus affect manual repolarization interval measurements in MCG. The errors detected demonstrate the importance of a standard presentation for repolarization measurement in the MCG.