Lipid peroxidation is an important process responsible for the flavor deterioration of many plant and animal foods. In order to understand possible mechanisms of initiation, a soybean lipoxygenase-polyunsaturated fatty acid model system was studied. The rate of enzyme-initiated oxidation was monitored by both oxygen consumption and diene conjugation. The hydroperoxides from an n-6 fatty acid, i.e. arachidonic, and n-3 fatty acids, i.e. linolenic, eicosapentaenoic, and docosahexaenoic acids were reduced and analyzed by reverse-phase high pressure liquid chromatography and gas chromatography/mass spectrometry. The lipoxygenase specifically catalyzed oxygenation at the n-6 carbon of both n-3 and n-6 fatty acids. Lipoxygenase activity was demonstrated in skin homogenate from rainbow trout and its role in off-flavor development is discussed.