Olive oil is one of the oldest known vegetable oils, and it is almost unique in that it can be consumed without any refining treatment. One of its most important quality problems is oxidative rancidity due to the oxygenation of polyenoic fatty acids and formation of compounds that derive from these fatty acid hydroperoxides. Beside autoxidation, lipoxygenases (LOXs) were suggested to be involved in this process. Here we show, that approximately 1.6% of all linoleic acid (LA) molecules within olive oil samples had been converted into LOX‐derived (13S,9Z,11E)‐13‐hydroperoxy‐9,11‐octadecadienoic acid (13‐HPODE) as determined by 1H NMR‐ and HPLC analysis. LOX activity tests indicated the occurrence of an active 13‐LOX exhibiting a pH optimum between pH 5.5 and 6.0. Furthermore, this enzyme preferentially metabolized free fatty acids. In order to elucidate the origin of this LOX, we analyzed olive endosperms for LOX forms. Chromatography of total protein extracts of the tissue showed LOX activity almost exclusively associated with a high molecular mass fraction. Light microscopic inspection, as well as the calculated phosphate, neutral lipid, and protein content of this fraction, suggested that this fraction may contain oil bodies and that LOX activity was associated with their membrane. This LOX activity had a pH optimum of 6.0. Activity assays at various temperatures indicated a significant catalytic efficiency of the enzyme up to 55°C. HPLC analysis of LA oxygenation products within the lipid fraction and of activity tests of isolated oil bodies showed that the LOX present in mature olive endosperm oil bodies was, as the enzyme from olive oil, a linoleate 13‐LOX preferentially active on free LA. We suggest, that this oil body LOX from olive endosperm, is the one detected originally in olive oil and may survive at least in part olive oil production.