Normally, the immune system functions as the body's defense against invading germs such as bacteria and viruses. In most allergic reactions, however, the immune system is responding to a false alarm. When an allergic person first comes into contact with an allergen, the immune system treats the allergen as an invader and gets ready to attack.

The immune system does this by generating large amounts of a type of antibody called immunoglobulin E, or IgE. Each IgE antibody is specific for one particular substance. In the case of pollen allergy, each antibody is specific for one type of pollen. For example, the immune system may produce one type of antibody to react against oak pollen and another against ragweed pollen. The IgE molecules are special because IgE is the only type of antibody that attaches tightly to the body's mast cells, which are tissue cells, and to basophils, which are blood cells. When the allergen next encounters its specific IgE, it attaches to the antibody like a key fitting into a lock. This action signals the cell to which the IgE is attached to release (and, in some cases, to produce) powerful chemicals like histamine, which cause inflammation. These chemicals act on tissues in various parts of the body, such as the respiratory system, and cause the symptoms of allergy.