Aldehydes and ketones produced from lipid peroxides (oxylipin carbonyls) exhibit a variety of biological activities ranging from the induction of defense genes to the irreversible damage to cells. Short oxylipin carbonyls such as acrolein and (E)-2-pentenal are responsible for tissue injury under environmental stress, but their production mechanism remains unclear. In this study, we elucidated the source fatty acids of short oxylipin carbonyls in leaves. We first established a comprehensive analysis of oxylipin carbonyls for quantitation and structural estimation. Carbonyls were extracted from rosette leaves of Arabidopsis thaliana, derivatized with 2,4-dinitrophenylhydrazine and separated with a reverse-phase HPLC equipped with a photodiode array detector and an Fourier transform ion cyclotron resonance mass spectrometer. Thirty-three distinct carbonyls were detected, in which 19 species were identified on the MS/MS spectrum. Using this analysis system, we compared the carbonyl composition in the leaves between two A. thaliana lines that have different fatty acid composition. The mutant fad7fad8, which lacks the biosynthesis of trienoic fatty acids in the plastid, contained significantly lower amounts of malondialdehyde, acrolein and (E)-2-pentenal and higher amounts of acetone, 3-pentanone, and n-hexanal than the wild type Col-0. This difference in the carbonyl composition agreed with the oxidative degradation of dienoic and trienoic fatty acids in vitro, showing that similar non-enzymatic reactions occur in the thylakoid membrane. Consideration of the formation mechanism of acrolein from trienoic fatty acid suggests that membrane lipids in chloroplasts are constitutively oxidized by singlet oxygen.