C-6-aldehydes are synthesized via lipoxygenase/hydroperoxide lyase action on polyunsaturated fatty acid (PUFA) substrates in plant leaves. The source pools and subcellular location of the processes are unknown. A close relationship is found between the composition of PUFA and the composition of C-6-aldehydes. In the current study, this relationship was tested using the Arabidopsis PUFA mutant lines act1, fad2, fad3 fad5, fad6, and fad7. The results indicate that C-6-aldehyde formation is influenced by the alteration of C-18 PUFA levels. Mutants act1 and fad5, which are deficient in C-16 unsaturated fatty acids, had wild-type levels of C-6-aldehyde production. Mutants deficient in the chloroplast hexadecenoic acid/oleic acid desaturase (fad6) or hexadecadienoic acid/linoleic acid desaturase (fad7) had altered C-6-aldehyde formation in a pattern similar to the changes in the PUFA. Mutations that impair phosphatidylcholine desaturase activity, such as fad2 and fad3, however, resulted in increased E-2-hexenal formation. The enzymes involved in C-6-aldehyde production were partially characterized, including measurement of pH optima. The differences in C-6-aldehyde formation among the fatty acid mutants of Arabidopsis appeared not to result from alteration of lipoxygenase/hydroperoxide lyase pathway enzymes. Investigation of the fatty acid composition in leaf phospholipids, glycolipids, and neutral lipids and analysis of the fatty acid composition of chloroplast and extrachloroplast lipids indicate that chloroplasts and glycolipids of chloroplasts may be the source or major source of C-6-aldehyde formation in Arabidopsis leaves.