We evaluated cold tolerance at the booting stage on the basis of seed fertility after cool-water treatment for three years (2005-2007) in 114 recombinant inbred lines (RILs) between temperate japonicas, Kirara397 (cold-sensitive) and Hatsushizuku (cold-tolerant). Composite interval mapping (CIM) was performed to identify quantitative trait locus (QTL) for cold tolerance. A QTL for cold tolerance at the booting stage was reproducibly detected in three trials on chromosome 1. Contribution of the QTL to the phenotypic variation ranged from 16.2 to 47.3%, and their additive effects were all towards Hatsushizuku. We also analyzed QTL for heading time and culm length, which are thought to affect cold tolerance. A QTL for heading time and that for culm length was detected every three years on the neighboring regions of chromosome 10, while no QTL for the two traits was detected on chromosome 1. These results suggest that the QTL on chromosome 1 has a major effect on the variation of cold tolerance between Kirara397 and Hatsushizuku without affecting heading time and culm length.