In order to investigate the genotypic differences in seed cadmium (Cd) concentration in soybean and rice, 17 soybean and 49 rice varieties were cultivated in Cd-polluted soils or water culture containing Cd. Significant differences in seed Cd concentration were found among soybean and rice varieties. A high level of inheritance of the seed Cd concentration was revealed for soybean. The physiological mechanism underlying the Cd translocation to shoots and seeds in soybean was involved in Cd retention in the roots. The commercial rice varieties (e.g., Koshihikari) were categorized into the low grain Cd group. On the other hand, several indica or indica-japonica rice varieties accumulated considerably high Cd concentrations in grains as well as straws, when they were cultivated under upland conditions, suggesting that these varieties would be most responsive to phytoremediation of Cd-polluted paddy fields. There was no correlation of the Cd concentration between younger shoots and mature seeds in the rice cultivars, so it may be impossible to use rice for evaluating the genotypic variation in seed Cd concentration using relatively younger shoots. On the other hand, a positive correlation between them was found in the soybean cultivars, so it may be possible to evaluate the genotypic variation in soybean seed Cd concentration using relatively younger soybean shoots. Interactions between Cd and other metals (Cu, Fe, Mn, and Zn) in terms of their uptake and translocation to shoots were found among the rice and soybean cultivars.