To reveal the genetic regions controlling eating quality of japonica rice and to establish a system for marker-assisted selection (MAS), we conducted a QTL analysis for eating quality of Koshihikari, a leading cultivar in Japan. We used a recombinant inbred population consisting of 92 lines derived from a cross between two closely related japonica cultivars, Moritawase (low eating quality) and Koshihikari. We evaluated overall eating quality (OE), glossiness (GL), taste (TA), stickiness (ST), and hardness (HD) of the lines over 3 years by sensory tests. QTL analysis revealed 43 QTLs on 16 regions across all chromosomes except chromosome 5. QTLs on chromosomes 1, 3, 6, 7, and 10 were detected in multiple years. The Koshihikari alleles at 37 QTLs increased the eating quality. Further QTL analysis revealed 8 QTLs for textural characteristics of cooked rice and 3 for the amino acid ratio of polished rice. Those on chromosomes 1, 3, 6, and 7 were located near the QTLs for eating quality.