Low temperature stress is common for rice grown in temperate regions and at high elevations in the tropics. The most senstive stage to this stress is booting, about 11 days before heading. Japonica cultivars are known to be more tolerant than indicas. We constructed a genetic map using 191 recombinant inbred lines derived from a cross between a temperate japonica, M-202, and a tropical indica, IR50, in order to locate quantitative trait loci (QTLs) conferring cold tolerance. The map with a total length of 1,276.8 cM and an average density of one marker every 7.1 cM was developed from 181 loci produced by 175 microsatellite markers. Cold tolerance was measured as the degree of spikelet sterility of treated plants at a 12 degrees C temperature for 5 days in the growth chamber. QTLs on chromosomes 1, 2, 3, 5, 6, 7, 9 and 12 were identified to confer cold tolerance at the booting stage. The QTL contribution to the phenotypic variation ranged from 11 to 17%. The two QTLs with the highest contribution to variation, designated qCTB2a and qCTB3, were derived from the tolerant parent, M-202, each explaining approximately 17% of the phenotypic variance. Two of the eight QTLs for cold tolerance were contributed by IR50.