In a previous study, we mapped 12 QTLs for 1,000 grain weight (TGW) in the 172 BC2F2 lines derived from a cross between Oryza sativa ssp. Japonica cv. Hwaseongbyeo and O. rufipogon. These QTLs explained 5.4 – 11.4% of the phenotypic variance for TGW. Marker-aided selection combined with backcrosses was employed to develop QTL-NILs for each QTL. BC2F2 lines with each target QTL were backcrossed to Hwaseongbyeo twice and then allowed to self to produce BC4F5 populations. SSR markers linked to TGW were employed to select QTL-NILs with the respective target QTL. Six QTL-NILs with the recurrent parent, Hwaseongbyeo were evaluated for nine traits for three years from 2007 and 2009. Differences were observed between each of the 6 QTL-NILs and Hwaseongbyeo in TGW. In addition to TGW, these QTL-NILs displayed differences in other agronomic traits possibly indicating a tight linkage of genes controlling these traits. The direction of the QTL for TGW in 6 QTL-NILs was consistent as in the BC2F2 lines from the same cross. Difference in TGW between each of the QTL-NILs and Hwaseongbyeo was associated with the difference in one or two grain shape traits; grain length, grain width, and grain thickness. SSR markers linked to the QTL for TGW will facilitate selection of the grain shape character in a breeding program to diversify grain shape and provide the foundation for map-based gene isolation. Also, the QTL-NILs developed in this report and the progenies from crosses between the QTL-NILs will be useful in clarifying epistatic interactions among QTLs for TGW.