Backcross inbred lines (BILs) derived from a cross of Nipponbare (japonica) / Kasalath (indica) // Nipponbare were used to identify quantitative trait loci (QTLs) controlling physico-chemical properties of rice grains such as amylose content (AC), alkali spreading score (ASS) and gel consistency (GC) by composite interval mapping over a period of two years. A total of 4 QTLs for AC were detected; qAC-5 and qAC-6 showed significant effects (hereafter referred to as “significant”) in both years, and qAC-6 explained more than 80 % of the phenotypic variance and was located in the wx region on the short arm of chromosome 6. The other 2 QTLs for AC with small additive effects were detected and were significant only in one year. Three QTLs for ASS were identified; qASS-6a and qASS-6b were significant in both years, and qASS-6a corresponded to a major gene located in the alk region on chromosome 6, while qASS-3 on chromosome 3 was significant only in one year. Five QTLs for GC were detected and all were significant only in one year. The lock of detection of major gene(s) for GC may be due to the fact that none of the parents were differentiated in terms of GC. These results showed that AC and ASS were mainly controlled by known gene loci, i.e., wx and alk, respectively, with modification by minor genes.