The ILSI Health and Environmental Sciences Institute Protein Allergenicity Technical Committee organized an international workshop in June 2006 in Estoril, Portugal, co-sponsored by the ILSI Research Foundation, ILSI International Food Biotechnology Committee and ILSI Europe. The objective was to discuss the effects of food processing on the allergenic potential of proteins and foods. The impact of food processing on the sensitization/induction phases of food allergy, and the bioavailability of allergens to the immune system were presented. Studies evaluating the stability, digestibility, and allergenicity of processed food allergens were identified, and their complexity and limitations discussed. Participants agreed that investigating food allergy mechanisms, validating appropriate methods for identifying allergenic proteins, and refining strategies to assess and manage the risks from food allergy were important before processing considerations are integrated into public-health decision-making for novel proteins. Other factors may also play a role in food allergy and include: food matrix; multiplicity of epitopes; geographic variation in patterns/prevalence of food allergies; and genetic factors, but required further exploration. Food processing may increase or decrease the intrinsic allergenicity of a protein, but current data do not facilitate the identification of specific variables that could be used to reliably determine how processing will influence protein allergenicity.