N(ε)-(hexanoyl)lysine (HEL) is known to be an oxidative lipid-decomposition product, and a powerful marker indicating oxidative stress in animal tissue. We investigated whether HEL could be useful as a marker in rice seeds damaged by oxidative stress during storage, as well as animals. We could show an accumulation of HEL in rice stored at high temperature (40 °C). This result significantly corresponded with an accumulation of TBARS. Rice germination deteriorated with non-enzymatic lipid peroxidation during storage at high temperature for a few months. These results suggested that a deterioration of rice germination ability resulted from oxidative damage caused by lipid peroxidation during storage. Moreover, HEL could become a useful marker for oxidative stress induced by lipid peroxidation. In addition, the activities of antioxidant enzymes, catalase and superoxide dismutase, significantly decreased in the rice seeds during storage at 40 °C. The relationship between accumulation of HEL and increases in antioxidant enzymes activities must be further studied. But, these results suggest that HEL might be a useful marker of oxidative stress in rice as well as in animals.