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Six japonica rice genotypes, differing in panicle type, grain density, and phytic acid (PA) content, were applied to investigate the effect of grain position on the concentrations of major mineral nutrients and its relation to PA content and grain weight within a panicle. Grain position significantly affected the concentrations of the studied minerals in both the vertical and horizontal axes of a rice panicle. Heavy-weight grains, located on primary rachis and top rachis, generally had higher mineral concentrations, but were lower in PA concentration and molar ratios of PA/Zn, compared with the small-weight grains located on secondary rachis and bottom rachis, regardless of rice genotypes. However, on the basis of six rice genotypes, no significant correlations were found among mineral elements, PA, and grain weight. These results suggested that some desired minerals, like Zn and Fe, and their bioavailability, can be enhanced simultaneously by the modification of panicle patterns, and it will be helpful in the selection of rice genotypes with low PA and high mineral nutrients for further breeding strategy without sacrificing their high yields.