We evaluated the effects of functional variation in three starch synthases in rice (Oryza sativa L.)−granule-bound starch synthase I (GBSSI, wx), starch synthase I (SSI, SSI), and starch synthase IIa (SSIIa, alk)−between indica cultivar Kasalath and japonica cultivar Nipponbare on starch properties and eating quality. We used three near-isogenic lines−NIL(Wxa), NIL(SSI k), and NIL(Alk)−containing chromosomal segments of Kasalath on a Nipponbare genetic background. The Wxa allele explained most of the difference in amylose content between the two cultivars, and decreased the peak viscosity and breakdown to less than half of those of Nipponbare. These changes reduced the quality of cooked rice both just after cooking and after storage at 5ºC. The variation in SSIIa also affected the eating quality after storage of cooked rice at 5ºC : NIL(Alk) became harder and less sticky than Nipponbare, although the rices were comparable just after cooking. Differential scanning calorimetry revealed faster retrogradation of the once-gelatinized starch in NIL(Alk). The variation in SSI alleles hardly affected these properties.