Food allergy is recognized as one of the major health concerns. It is estimated that ca. 4% of the population is affected by food allergenic disorders. Food allergies are defined as IgE-mediated hypersensitivity reactions. Foods such as peanuts, tree nuts, wheat, soy, cow's milk, egg, fish and shellfish are regarded as responsible for the majority of reactions. The ubiquitous presence of allergens in the human foods coupled with an increased awareness of food allergies warrants to undertake appropriate preventive measures for protecting sensitive consumers from unwanted exposure to offending food allergens. 2-DE followed by immunoblotting and identification of IgE-reactive proteins, as a proteomic approach to identify new allergens in foods, are reviewed. Specific examples of identification of allergens in foods and beverages by using 2-DE and IgE are described. Protein profiling using 2-DE and allergens detection by IgE has become a powerful method for analyzing changes of allergens content in complex matrix during food processing.