Food allergy is a global health concern. Most food allergens are proteins which, even in small quantities, can cause an allergic reaction in sensitized persons. For the provision of food information to consumers, food products containing any of 14 food allergens must be labelled according to Regulation (EU) no. 1169/2011 of the European Parliament. Food preparation often employs high temperatures to improve conservation. Prolonged heat treatment, however, can alter food molecules. Food manufacturers and food agencies carry out tests to determine the absence of undeclared allergenic substances in food products. Laboratory tests are based on enzyme immunoassay (ELISA-based) or molecular biology (PCR-based) techniques in which proteins are the target molecules, and a portion of DNA is a marker of the allergenic ingredient, respectively. With this study we wanted to determine the effect of heat treatment on almond and hazelnut allergens. To do this, we compared the ability of the two techniques to detect allergenic proteins at different temperatures and duration of heating. The allergenic potential of almond and hazelnut ingredients after heating is crucial to consumer health and safety.