Normally, the immune system functions as the body's defense against invading agents (bacteria and viruses, for instance). In most allergic reactions, however, the immune system is responding to a false alarm. When allergic persons first come into contact with an allergen, their immune systems treat the allergen as an invader and mobilize to attack. The immune system does this by generating large amounts of a type of antibody (a protein) called immunoglobulin E, or IgE. (Only small amounts of IgE are produced in nonallergic people.) Each IgE antibody is specific for one particular allergen. In the case of pollen allergy, the antibody is specific for each type of pollen: one antibody may be produced to react against oak pollen and another against ragweed pollen, for example.

These IgE molecules attach themselves to the body's mast cells, which are tissue cells, and to basophils, which are cells in the blood. When the enemy allergen next encounters the IgE, the allergen attaches to the antibody like a key fitting into a lock, signaling the cell to which the IgE is attached to release (and in some cases to produce) powerful inflammatory chemicals like histamines, prostaglandins, leukotrienes, and others. The effects of these chemicals on various parts of the body cause the symptoms of allergy.