Food allergies are an immune-system reaction to protein molecules found on 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, leading to all of the reactions known as symptoms of an allergy. For a true food allergy, reaction time is usually within minutes to two hours.