The immune system normally protects the body from foreign invaders that cause harm such as viruses and bacteria. During an allergic reaction the immune system turns its defenses against a substance that does not normally cause disease, one that is ignored by the immune system of people without allergies, resulting in the symptoms of allergies.

When a person with allergies encounters an allergen, the immune system generates a large quantity of a type of defense molecule called an IgE antibody to bind to allergen. Each IgE antibody is specific to a particular allergen so a person who is allergic to cat dander but not to dog dander would have large quantities of IgE antibodies that recognize cat dander, but none that recognize dog dander.

After the initial exposure to an allergen, the IgE antibodies that are produced can attach themselves to immune system cells called mast cells. When this happens, these mast cells become primed and ready to be activated. When the person next encounters that allergen, it will bind to the IgE antibodies attached to primed mast cells, signaling the mast cells to release large amounts of histamine and other chemicals that cause inflammation. It is these chemicals that cause the symptoms of allergies.

If the allergen is airborne, it will most likely be encountered in the nose, eyes, or possibly the lungs, leading to symptoms of inflammation in those areas. If the allergen is a food or drug, the reaction often occurs in the mouth, throat or gastrointestinal tract.