Grain size is one important trait in the agronomics of rice production. Although several quantitative trait loci (QTLs) controlling the length, width, and thickness of rice grains have been genetically identified, and some have been cloned, the molecular mechanisms of grain size regulation are still unclear. To identify the genetic factors affecting rice grain length, we performed QTL analysis using an F2 population and F3 lines derived from a cross between two Oryza sativa L. varieties: the long-grain japonica cultivar ‘Cytoto’ and the indica variety ‘Kasalath’. Three QTLs for grain length were detected, one each on chromosomes 3, 4 and 7. The presence of the Cytoto-type allele at any of the three loci was associated with increased grain length. Analysis of the QTL detected on chromosome 4, designated qGL4b, using F3 progeny confirmed an allelic difference between ‘Cytoto’ and ‘Kasalath’ at qGL4b. The Cytoto allele of qGL4b appears to increase the length and weight of the rice grain.