Some time after they are exposed to peanuts, a small number of people start to develop allergic antibodies (the class of antibody is called "IgE") that specifically recognize chemical structures found in peanut proteins. These "Y"-shaped antibody molecules float in the blood until they encounter a "mast cell," an important component of allergic reactions that is found scattered in almost all tissues. The antibody molecules anchor themselves (at the base of the "Y") to the surface of the cell. There they wait until a floating fragment of peanut protein shows up. When the fragment, which might have been inhaled or swallowed, encounters two adjoining IgE molecules, it forms a bridge and attaches to both of them. This begins a Rube Goldberg sequence of events in which the molecules are pulled toward each other and a kind of message is passed down through the body of the "Y," causing them to set off a signal that passes through the membrane enclosing the mast cell. This signal, in turn, causes microscopic sacks of chemicals deep inside the cell to swell, rise to the surface, and release their contents into the environment of the cell.

Histamine is the most important of the many active chemicals released. The released histamine causes nearby small blood vessels to leak, flooding the surrounding tissues with fluid. If the leaking happens just under then skin, swelling occurs and hives appear. But if the reaction is more widespread and happens simultaneously at many locations, then something much worse occurs: The huge loss of fluid from inside blood vessels throughout the body causes an instantaneous and catastrophic drop in blood pressure. This is anaphylactic shock. If it is severe, circulation fails, depriving tissues everywhere (including the brain) of oxygen.

Mast cells activated by this mechanism also release other potent chemicals that can cause an asthmalike response in the lungs, complicating the anaphylactic shock. In addition, swelling in the back of the throat caused by fluid leakage can be so severe that the entire upper airway closes off, causing suffocation.