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Chalk, an opaque area in the rice grain, is an important quality characteristic in rice and occurs most commonly when grains are exposed to high temperatures during development. Chalky rice decreases the value of rice because of its undesirable appearance and eating quality for consumers. We investigated the chemical composition, morphological structure, cooking, texture properties of cooked rice, and pasting and gelatinization properties to evaluate the reason for the deterioration in eating quality of chalky rice. The ultra-structure of chalky kernels differed greatly from that of head rice. Chalky grain had more air spaces, a disordered cellular structure, and rounder amyloplasts than head rice. Chalky rice absorbed water more rapidly during cooking and had a slightly larger expansion volume than head rice, confirming its loose starch granule structure. The lower amylose content of chalky kernels caused a more soluble solid and higher iodine index during cooking indicating their lower eating quality compared to translucent kernels. The lower gelatinization temperature of chalky kernels was suggested to be related to a more short-branch chain amylopectin structure. Chalky kernels resulted in a harder and less adhesive (or sticky) texture of cooked rice, requiring more time for chewing than those of head kernels, caused by its low protein content. The palatability of cooked rice showed a linear decrease with increasing chalky rice proportion in the sensory evaluation. In amylography, the peak and final viscosities greatly decreased when the chalky rice proportion increased from 0 to 5%. It indicated that chalky rice kernels induce quality deterioration even at 5%.