The quantitative trait loci (QTLs) for cold tolerance during early growth period were identified using a F2:3 population (including 200 individuals and lines derived from a cross between indica rice and japonica rice ’Milyang 23/Jileng 1’) with microsatellite markers. The cold tolerance at the seedling and tillering stages, and the growth ability of seedling under low temperature conditions were evaluated. All of the traits associated with cold tolerance at early growth stages appeared a continuous distribution near to normal in F3 lines, these were inherited as quantitative traits controlled by polygenes. Three QTLs on chromosomes 1, 5 and 9, which associated with cold tolerance at the seedling stage were detected. Among them, qCTS1 accounted for 15.5% of observed phenotypic variation; Five QTLs on chromosomes 2, 3, 7, 9 and 11, associated with cold tolerance at the tillering stage were found, which explained lower percentage of observed phenotypic variation; Four QTLs on chromosomes 1, 2, 11 and 12, which associated with the growth ability of seedling under low temperature conditions were found, among them, qGAS2and qGAS12 explained 26.6 and 42.9% of observed phenotypic variation, respectively, which were major genes. The quantitative trait loci (QTLs) for cold tolerance during early growth period were identified using F2: 3 population (including 200 individuals and lines derived from a cross between indica rice and japonica rice ’Milyang 23 / Jileng 1’) with microsatellite markers. The cold tolerance at the seedling and tillering stages, and the growth ability of seedling under low temperature conditions were... All of the traits associated with cold tolerance at early growth stages appeared a continuous distribution near to normal in F3 lines, these were inherited as Quantitative traits controlled by polygenes. Three QTLs on chromosomes 1, 5 and 9, which associated with cold tolerance at the seedling stage were detected. Among them, qCTS1 accounted for 15.5% of observed phenotypic variation; Five QTLs on chromosomes 2, 3, 7 , 9 and 11, associated with cold tolerance at the tillering stage were found, which explained lower percentage of observed phenotypic variation; Four QTLs on chromosomes 1, 2, 11 and 12, which associated with the growth ability of seedling under low temperature conditions were found, among them, qGAS2 and qGAS12 explained 26.6 and 42.9% of observed phenotypic variation, respectively, which were major genes.