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Soybean and hazelnut represent major food allergens. Their inadvertent presence in foods might pose a serious threat to allergic consumers. Therefore, reliable detection methods are needed. Commercial enzyme-linked immunosorbent assays (ELISA) are the preferred methods especially by the food industry and enforcement agencies for the detection of contamination levels of food allergens. However, they are susceptible to erroneous results due to the modification of the allergens (proteins) during food processing. In this paper, the impact of protein oxidation on the detectability of soybean and hazelnut was investigated. Lipid-induced oxidation did not have a great impact on the detectability while the more severe hypochlorous acid-induced oxidation led to dramatic decrease in detectability for both hazelnut and soybeans. The observed impact was highly dependent on the type of ELISA kit used.