Prostaglandin-like compounds, called isoprostanes, are generated by free enzyme-independent radical peroxidation of the acids arachidonic (AA), eicosapentaenoic (EPA) and docosahexaenoic (DHA). Up to now, isoprostanes have been largely studied only in men and biological systems, but never in food. In this research, cod liver oil was used as a model system to study the oxidation mechanism in food containing high amounts of EPA and DHA. For comparison, under similar oxidation conditions, also the behaviour of a sunflower seed oil and an n-3 long-chain polyunsaturated fatty acid capsule supplement oil were studied. It was ascertained that EPA- and DHA-derived compounds were formed during oxidation. These compounds were polar and easily isolatable by methanol from oxidised transmethylated oil. EPA and DHA oxidation derivatives showed maximal absorbance at 200 nm and were very potent pro-oxidants at high temperatures. In oxidised sunflower oil, similar compounds did not form. Unfortunately, the chemical structures of the EPA and DHA oxidation derivatives were not discovered, but it is a realistic hypothesis that they could be isoprostane-like compounds.