Cadmium (Cd) poses a serious risk to human health due to its biological concentration through the food chain. To date, information on genetic and molecular mechanisms of Cd accumulation and distribution in rice remains to be elucidated. We developed an independent F7 RIL population derived from a cross between two japonica cultivars with contrasting Cd levels, 'Suwon490' and 'SNU-SG1', for QTLs identification of Cd accumulation and distribution. 'Suwon490' accumulated five times higher Cd in grain than 'SNU-SG1'. Large genotypic variations in Cd accumulation (17-fold) and concentration (12-fold) in grain were found among RILs. Significant positive correlations between Cd accumulation in grain with shoot Cd accumulation and shoot to grain distribution ratio of Cd signify that both shoot Cd accumulation and shoot to grain Cd distribution regulate Cd accumulation in japonica rice grain. A total of five main effect QTLs (scc10 for shoot Cd accumulation; gcc3, gcc9, gcc11 for grain Cd accumulation; and sgr5 for shoot to grain distribution ratio) were detected in chromosomes 10, 3, 9, 11, and 5, respectively. Of these, the novel potential QTL sgr5 has the strongest effect on shoot to grain Cd distribution. In addition, two digenic epistatic interaction QTLs were identified, suggesting the substantial contribution of nonallelic genes in genetic control of these Cd-related traits.