Food allergies are an immune-system reaction to protein molecules found in food. This reaction is actually a mistake your body makes. Your immune system is set up to defend your body against viruses, toxins, and bacteria — foreign invaders that have no place in the body. When cells in your body think of food as a foreign invader they attack, producing the reactions known as symptoms of an allergy. In the case of a true food allergy, reaction time is usually within minutes to two hours.