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Comparison of biomagnetic measurements performed with different multichannel magnetometers is difficult, because differing sensor types and locations do not allow measurements from the same locations in respect to the body. In this study, two transformation procedures were utilized to compare magnetocardiograms (MCG) recorded with two different multisensor systems. Signals from one sensor array were used to compute parameters of a multipole expansion or minimum-norm estimates at 1-ms steps over the cardiac cycle. The signals of the second sensor array were then simulated from the computed estimates and compared against measured data. Both the multipole- and the minimum-norm-based transformation method yielded good results; the average correlation between simulated and measured signals was 93%. Thus, the methods are useful to compare MCG recordings performed using differing sensor configurations, e.g., for multicenter patient studies. This study provides the first empirical basis for assessing the transformation of MCG data of differing devices by general model-based field reconstructions.