BACKGROUNDThe oxidative deterioration of vegetable oils is commonly measured by the peroxide value, thereby not considering the contribution of individual lipid hydroperoxide isomers, which might have different bioactive effects. Thus, the formation of 9‐ and 13‐hydroperoxy octadecadienoic acid (9‐HpODE and 13‐ HpODE), was quantified after short‐term heating and conditions representative of long‐term domestic storage in samples of linoleic acid, canola, sunflower and soybean oil, by means of stable isotope dilution analysis–liquid chromatography‐mass spectroscopy.RESULTSAlthough heating of pure linoleic acid at 180 °C for 30 min led to an almost complete loss of 9‐HpODE and 13‐HpODE, heating of canola, sunflower and soybean oil resulted in the formation of 5.74 ± 3.32, 2.00 ± 1.09, 16.0 ± 2.44 mmol L–1 13‐HpODE and 13.8 ± 8.21, 10.0 ± 6.74 and 45.2 ± 6.23 mmol L–1 9‐HpODE. An almost equimolar distribution of the 9‐ and 13‐HpODE was obtained during household‐representative storage conditions after 56 days, whereas, under heating conditions, an approximately 2.4‐, 2.8‐ and 5.0‐fold (P ≤ 0.001) higher concentration of 9‐HpODE than 13‐HpODE was detected in canola, soybean and sunflower oil, respectively.CONCLUSIONA temperature‐dependent distribution of HpODE regioisomers could be shown in vegetable oils, suggesting their application as markers of lipid oxidation in oils used for short‐term heating. © 2017 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.