We compared three QSM reconstruction algorithms for use in the upper abdomen: the water-fat separation method (WF), MUDICK, and iLSQR. A healthy male was scanned nine times, in different positions, and three QSM reconstructions from the same source data were compared. The intra-scan SD, representing image homogeneity among images, and the inter-scan SD, representing repeatability among scans, were lower in WF than in MUDICK and iLSQR. Thus, the WF method yielded better homogeneity and repeatability for susceptibility values in the upper abdomen. This forms the basis for further clinical studies and applications of QSM in the abdomen.