Quantitative trait loci (QTL) for percentage of chalky grain, degree of chalkiness, and endosperm transparency were detected using 3 recombinant inbred line populations derived from crosses between parental lines of commercial three-line hybrids of indica rice. Two of the populations showed great variations on heading date, and the other had a short range of heading date variation. A total of 40 QTLs were detected and fell into 15 regions of 10 chromosomes, of which 5 regions were detected for 1 or more same traits over different populations, 2 were detected for different traits in different populations, 3 were detected for 2 or all the 3 traits in a single population, and 5 were detected for a single trait in a single population. Most of these QTLs have been reported previously, but a region located on the long arm of chromosome 10 showing significant effects in all the 3 populations has not been reported before. It was shown that a number of gene cloned, including the Wx and Alk for the physiochemical property of rice grain, and GW2, GS3 and GW5 for grain weight and grain size, could have played important roles for the genetic control of grain chalkiness in rice, but there are many more QTLs exerting stable effects for rice chalkiness over different genetic backgrounds. It is worth paying more attentions to these regions which harbor QTL such as the qPCG5.2/qDC5.2/qET5.2 and qPCG10/qDC10/qET10 detected in our study. Our results also showed that the use of segregating populations having high-uniform heading date could greatly increase the efficiency of the identification of QTL responsible for traits that are subjected to great environmental influence.