Phobias are more often than not linked to the amygdala, an area of the brain located behind the pituitary gland in the limbic system. The amygdala secretes hormones that control fear and aggression, and aids in the interpretation of this emotion in the facial expressions of others. When the fear or aggression response is initiated, the amygdala releases hormones into the body to put the human body into an "alert" state, in which they are ready to move, run, fight, etc  
 
Studies have shown a difference between the response cycles of those facing an object of a phobia and those facing a dangerous object that does not trigger phobia-like responses. In one case, patients with arachnophobia were shown pictures of a spider (the object of fear) and a snake (a control picture, intended to induce the normal response). When flashed up, the arachnophobe responded with brief fear to the snake, but the amygdala quickly shut down when the logical areas of higher thought analyzed the threat and ruled it out as unimportant. However, when shown the spider, the arachnophobe's amygdala reacted, and then did not stop secreting 'alarm' hormones, even after they had rationalized the situation they were in  
 
For this reason, a phobia is generally classified as a panic disorder by most psychologists, since it involves an unnatural or illogical functioning of the brain.