Biodiesel is commonly considered as a safe fuel because of the low toxicity of biodiesel components and a high flash point. However, autoxidation of fatty esters is possible during storage. Therefore, we analysed soybean biodiesel stored at room temperature for 5 years and soybean biodiesel obtained by accelerated oxidation, by gas chromatography-mass spectrometry. The main degradation products were hexanal, 2-heptenal and 2,4decadienal, which increase the toxicity of biodiesel. We therefore identified for the first time toxic compounds from biodiesel degradation during storage.