Accumulation of Cd in rice grain is a serious concern of food safety since rice as a staple food is a major source of Cd intake in Asian countries. However, the mechanisms controlling Cd accumulation in rice are still poorly understood. Herein, we report both physiological and genetic analysis of two rice cultivars contrasting in Cd accumulation, which were screened from a core collection of rice cultivars. The cultivar Anjana Dhan (Indica) accumulated much higher levels of Cd than Nipponbare (Japonica) in the shoots and grains when grown in both soil and solution culture. A short-term uptake experiment (20 min) showed that Cd uptake by Nipponbare was higher than that by Anjana Dhan. However, the concentration of Cd in the shoot and xylem sap was much higher in Anjana Dhan than in Nipponbare. Of the Cd taken up by the roots, <4% was translocated to the shoots in Nipponbare, compared with 10-25% in Anjana Dhan, indicating a higher root-to-shoot translocation of Cd in the latter. A quantitative trait locus (QTL) analysis for Cd accumulation was performed using an F(2) population derived from Anjana Dhan and Nipponbare. A QTL with large effect for Cd accumulation was detected on the short arm of chromosome 7, explaining 85.6% of the phenotypic variance in the shoot Cd concentration of the F(2) population. High accumulation is likely to be controlled by a single recessive gene. A candidate genomic region was defined to <1.9 Mb by means of substitution mapping.