Hypersensitive cell death is an important defense reaction of plants to pathogen infection and is accompanied by lipid peroxidation processes. These may occur non-enzymatically by the action of reactive oxygen species or may be catalyzed by enzymes such as alpha-dioxygenases, lipoxygenases, or peroxidases. Correlative data showing increases in 9-lipoxygenase products in hyper-sensitively reacting cells have so far suggested that a large part of lipid peroxidation is mediated by a specific set of 9-lipoxygenases. To address the significance of 9-lipoxygenases for this type of pathogen response in potato, RNA interference constructs of a specific pathogen-induced potato 9-lipoxygenase were transferred to potato plants. Significantly reduced 9-lipoxygenase transcript levels were observed in transgenic plants after pathogen treatment. In addition, 9-lipoxygenase activity was hardly detectable, and levels of 9-lipoxygenase-derived oxylipins were reduced up to 12-fold after pathogen infection. In contrast to wild type plants, high levels of non-enzymatically as well as 13-lipoxygenase-derived oxylipins were present in 9-lipoxygenase-deficient plants. From this we conclude that during the normal hypersensitive response in potato, lipid peroxidation may occur as a controlled and directed process that is facilitated by the action of a specific 9-lipoxygenase. If 9-lipoxygenase-mediated formation of hydroperoxides is repressed, autoxidative lipid peroxidation processes and 13-lipoxygenase-mediated oxylipins synthesis become prominent. The unaltered timing and extent of necrosis formation suggests that the origin of lipid hydroperoxides does not influence pathogen-induced cell death in potato.