The amygdala, so named because it resembles an almond, is a set of nuclei in the brain located closely to each other and therefore grouped under the same name. Among the most prominent are the basolateral complex, the centromedial nucleus, and the cortical nucleus. The amygdala is part of the limbic system, responsible for regulating the emotions. The amygdala is most commonly associated with the emotions of fear and anxiety, and its size is positively correlated to the level of aggression in a given species. It is also associated with the emotion of pleasure, though mainly in a negative sense, i.e., the pleasure sometimes inherent in aggression.

There are two amygdalas, symmetrically arranged near the center of the brain, just above the hypothalamus. They are each about one inch in length. The amygdala has received much attention in recent decades, and has been the focus of many research projects.

The amygdala plays a key part in what has been called the "general-purpose defense response control network" and reacts in response to unpleasant sights, sensations, or smells. Anger, avoidance, and defensiveness are emotions activated largely by the amygdala. Its evolutionary origins lie with the early fishes, and it has direct connections to one of the oldest sensory areas, the olfactory bulb. The amygdala is responsible for activating ancestral signs of distress such as "tense-mouth" and defensive postures such as crouching.

Like many parts of the limbic system, the functioning of the amygdala is not purely associated with any one emotion. Poor amygdalic functioning has been associated with anxiety, autism, depression, narcolepsy, post-traumatic stress disorder, phobias, and schizophrenia. Lesion studies with monkeys have shown that when the amygdala is impaired before six months of age, individuals have difficulty adapting to social life. This is because the amygdala is necessary not just for experiencing emotions like fear, but also for modeling and quickly recognizing the presence of these emotions in others. Thus a damaged amygdala has become associated with the condition of autism, or social-blindness.

In humans the amygdala is the brain structure that varies most widely between the sexes. When males are castrated, the size of their amygdala shrinks by 30%. Depression has been associated with asymmetrical amygdala sizes.