Rice spotted leaf 6 (spl6) mutant produces lesions caused by spontaneous cell death in the absence of pathogenic infection. Expression of this genetic trait was developmentally programmed. After the tillering stage, small red and brown lesions were initiated in groups on the leaf blade. Eventually, the lesions formed parallel lines along the midrib of the leaf. Under light and transmission electron microscopy, we observed that thylakoid membranes of mesophyll chloroplasts were progressively damaged in the nonspotted section of the mutant leaf. However, chloroplasts were absent in the mesophyll cells of the spotted area of the spl6 mutant. These results indicated that lesion formation of the spl6 mutant might be caused by oxidative burst. Proteome analysis revealed that 159 protein spots were up or downregulated in comparison between spotted leaves of the spl6 mutant plants and normal leaves of the wild type. Among them, protein disulfide isomerase (PDI), transketolase, thioredoxin peroxidase (TPX), ATP synthase, RuBisCO large subunit, and RuBisCO activase small subunit were not identified in the spl6 mutant but were abundant in the wild type. Especially, the absence of TPX and PDI might be the cause of the failure to protect cells against oxidative burst resulting in degradation of the thylakoid membranes and leading to programmed cell death and lesion development.