Low temperatures cause a decrease in seed yield and deterioration of seed quality in soybeans and have threatened stable soybean production in cool areas. To overcome this problem, physiological and genetic analyses have been conducted as steps towards the development of efficient breeding systems. Several evaluation methods that are useful for physiological studies as well as for genetic screening have been developed. Low temperature treatment for four weeks or longer starting at the first flowering stage in plants was found to reduce all of the yield components and result in genotypic variation in chilling tolerance for seed yield during reproductive growth. Analysis of low seed fertility induced by low temperature treatment prior to flowering revealed that the tetrad stage during pollen development is the most sensitive to chilling. Browning of seed coats, a major factor causing deterioration of seed quality, was induced most severely by low temperature treatment about one week after flowering. In addition, several genetic loci associated with chilling tolerance have been identified. Cultivars and lines with the T allele at the T locus, which controls the color of pubescence, have repeatedly been demonstrated to exhibit better chilling tolerance than those with the other allele, t. Maturity loci controlling flowering time and maturity such as E1, e3 and e4 were also found to be associated with chilling tolerance for both seed yield and quality. However, evidence showing that these loci are directly involved in chilling tolerance remains to be provided.