The agents that cause IgE-mediated allergies are known as allergens and are almost always proteins. It is emerging that the way in which food proteins elicit an allergic reaction can be modified by food processing procedures. This is because food processing alters the structure of food proteins through either unfolding and aggregation, or covalent modification by other food components such as sugars. In this way the IgE-recognition sites on an allergen, known as epitopes, can either be destroyed or new epitopes formed. Processing can destroy the allergenicity of some proteins, notably the Bet v 1 homologues, which both unfold and become modified with plant polyphenols. Others, such as the prolamin superfamily members, the nsLTP and 2S albumin allergens, have stable protein scaffolds and either do not unfold or re-fold on cooling, retaining their allergenicity. Some allergens are highly thermostable because of their mobile structures which are not disrupted on heating, such as the caseins and seed storage prolamins of wheat. Others, such as seed storage globulins, only partially-unfold and can retain much of their allergenicity. The structure of the food matrix may also affect the release and stability of allergens impacting on the elicitation of reactions in food allergic individuals. Such complexity makes it a challenge to develop generic food processing procedures capable of removing or reducing allergenicity which are effective for all allergic consumers. A better knowledge of how processing affects the allergenicity of food is also important for risk assessors and managers involved in managing allergenic hazards in food.