Abstract: Chilling injury of rice seedling under natural field conditions is one of the most important limiting factors for rice production in many rice cropping regions.In the present study, seedling cold tolerance at 3 leaf stage of 81 doubled haploid (DH) lines derived from an indica japonica cross (indica cv.'Gui630'/japonica cv.'02428') of rice was investigated.The data combined with a previously constructed RFLP linkage map were used to map QTLs conferring seedling cold tolerance by a computer program QTLMapper1.0 based on mixed linear models.A total of 3 main effect QTLs and 8 epistatic loci for seedling cold tolerance were detected.Of which, 3 main effect QTLs individually accounted for 7.9%,18.3% and 24.4% of the total phenotypic variation respectively and they collectively explained 42.3% of the total phenotypic variation.These three QTLs were located onto rice chromosome 3,11 and 12 respectively and their positive alleles were all derived from the japonica parent '02428'.Among 8 epistatic loci,there were two pairs of epistatic interactions individually accounted for more than 15% of the phenoty pic variation and their two locus recombinants (interactions between alleles from the different parent) had positive effects.Great difference between the two parents in seedling cold tolerance was observed.Continuous variation and aggressive segregation for the trait were displayed in the 81 DH lines.These results suggested that the seedling cold tolerance of rice be quantitatively inherited and epistasis be one of major factors as its genetic basis.