In this review of research priorities, presented for the European Commission, food allergy is established as a disease with a considerable impact on modern society. Research paradigms have changed from establishing basic symptomatology and diagnostic methods over allergen characterization to a risk-identification approach looking at which patients are at risk of developing reactions to a certain dose of allergenic food. In order to solve some of the apparent paradoxes of regional, temporal, and species-related differences in sensitization and food allergic reactions, it is suggested to study the basic underlying mechanisms in the cross-field between immunology and gastroenterology. Research priorities should include the molecular basis of cross-reactivity, the digestion and maintenance of antigenicity, the genetics of food allergy, and the immune response to food antigens and effects on the gastrointestinal immune system by food matrices and the microbial gut-flora. Necessary methods with be spanning from molecular biology to large-scale clinical and epidemiological studies.