Several quantitative trait loci (QTLs) associated with the apparent quality of brown rice were identified. QTL analysis was carried out using F₂ and F₃ populations derived from a cross between two japonica varieties, Hana-echizen (high quality of brown rice) and Niigatawase (low quality with numerous white-back and basal-white kernels). F₂ individuals were grown in paddy fields in 2003, and F₃ lines were grown in paddy fields and in a greenhouse to expose them to high temperature stress during the ripening period in 2004. Apparent quality of brown rice was evaluated based on the percentage of white-back and basal-white kernels. Two putative QTLs associated with white-back kernels in the F₂ population grown under low temperature conditions in paddy fields in 2003 were identified on chromosomes 3 and 6. The closest SSR markers were RM4512 and RM3034, respectively. One putative QTL associated with basal-white kernels in the F₂ population was identified on chromosome 6. The closest marker was RM3034. Two putative QTLs associated with white-back kernels in the F₃ population grown under high temperature conditions in paddy fields in 2004 were identified on chromosomes 4 and 6. The closest SSR markers were RM3288 and RM3034, respectively. One putative QTL associated with white-back plus basal-white kernels in the F₃ population grown under high temperature stress in the greenhouse was identified on chromosome 6. The closest marker was RM3034. The QTLs identified near RM3034 on the short arm of chromosome 6 contributed most to the apparent quality of brown rice. The QTLs identified near RM4512 and RM3288 which also affected the apparent quality of brown rice, were detected in either the F₂ or F₃ population. The QTLs identified in the present study should be useful for marker-assisted selection to breed varieties with a high apparent quality of brown rice, especially varieties with tolerance to kernel damage due to high temperature stress during the ripening period.