The amygdala is involved in producing and responding to non-verbal signs of anger, fear and defensiveness. Learning and responding to stimuli that warn of danger involves neural pathways that send information about the outside world to the amygdala, which in turn, determines the significance of the stimulus and triggers emotional responses like freezing or fleeing as well as changes in the inner workings of the body's organs and glands.

Damage to the amygdala interferes with the effects of emotions on memory. If the amygdala is severed from the rest of the brain, the result is a striking inability to gauge the emotional significance of events, a condition called 'affective blindness': growls, screams, angry voices, and other negative signs may lose their meaning and become incomprehensible as afferent cues.

There is growing evidence that indicates that the amygdala enhances and directs our perception and attention regarding emotions other than fear pleasure or disgust, for instance calling to attention key parts of our brains and making them more responsive in forming memories and associations. By attuning the brain to all manner of threats and pleasures not just the snake on the path but the scowl on your boss's face and the smile on your child's the amygdala thus helps confer emotional significance on a wide range of experience. We've known for decades that fears are extinguished not because they fade, but because new, less threatening associations take their place. The rat hears a once-threatening sound repeatedly without pain, and a neutral association slowly replaces the fearful one. You hear often enough the once-lacerating song you long ago enjoyed with your ex-lover, it loses its bite. Researchers have recently found that this process relies on a calming of the amygdala via the medial prefrontal cortex.

What is known about the amygdala is that it has a dual sensory input system. Both inputs run from the eyes, ears, and other sense organs to the thalamus. At that point the inputs diverge. One pathway leads directly to the amygdala while the other first passes through the cortex. Each input causes a distinct and specialized behaviour. The amygdala is specialized for reacting to stimuli and triggering a physiological response, a process that would be described as the "emotion" of fear. After this, the stimuli of the activation of the amygdala is transmitted to the cortex. This is a distinct difference from a conscious feeling of fear.

One could say that a life without amygdala is a life stripped of personal meanings. Animals that have their amygdala removed or severed lack fear and rage, lose the urge to compete or cooperate, an no longer have any sense of their place in their kind's social order; emotion is blunted or absent.

In the book 'Questions about emotions', Paul Ekman and Richard Davidson describe the case of a man whose amygdala had been surgically removed to control severe seizures. He became completely uninterested in people, preferring to sit in isolation with no human contact. While he was perfectly capable of conversation, he no longer recognized close friends, relatives or even his mother and remained impassive in the face of their anguish at his indifference. Without an amygdala, he seemed to have lost all recognition of feelings as well as any feeling about feelings.

After the central nucleus has been destroyed, animals no longer show signs of fear when confronted with stimuli of adverse events. As a result, their blood level of stress hormones is lower. Neurons of the central nucleus send axons to region of the brain responsible for the expression of the various components of emotional responses to aversive stimuli. The aversive stimuli would elicit non-specific responses controlled by the autonomic nervous system (eyes dilate; heart rate and blood pressure increase; breathing increases and there is secretion of stress-related hormones). These results suggest that the autonomic and endocrine responses controlled by the central nucleus are responsible for the harmful effects of long-term stress. Physical changes such as freezing when facing aversive stimuli, take place in the lateral nucleus of the amygdala.
Occasionally, there can be debilitating problems associated with hyperactivity of the amygdala. Being the storehouse for the memory of fear, it can misinterpret signals from the body and cause inappropriate actions. This can lead to panic. Panic is a heightened stage of anxiety and fear feeding itself in a positive feedback loop and jumping to faulty conclusions, which focus on impending danger, madness, harm, or death. Physically, the body undergoes many changes that ready it for extreme action. There is a marked secretion of glucocorticoids and catecholamines which increases the blood glucose levels. Also, increase production of epinephrine and norepinephrine, which has the effect of vasodilation of blood vessels in skeletal muscles. Other symptoms of the sympathetic-adrenergic stimulation involve modifications of breathing, increased temperature, localized sweating, decreased motility of the stomach, bowels, and intestines, constrictions of sphincters in the stomach and intestines, as well as piloerection (little hairs stand up) when attention is shifted away from the anxiety-provoking stimulus, less fear is observed.

Antonio Damasio's research has found that patients whose link between the amygdala and neocortex has been damaged exhibit extremely poor decision-making skills. The amygdala is a storehouse of emotional reactions. People without access to this storehouse are rather like a rambler without a compass; they can spot alternative paths, but they have no idea how to evaluate them. The amygdala can sometimes cause emotional dumbness, as with over-hasty actions and emotional hijackings, but Damasio's research suggests that it is also required for emotional wisdom. We need to train and listen to the amygdala, not suppress it. For example, freezing is often the first thing people and other animals do when sudden danger appears. Predators respond to movement, so freezing is overall probably the best single thing to do first, at least it was for our distant ancestors. If they had to think about what to do first, they'd have been so caught up in the thought process they'd probably fidget around and then get eaten.

The connection to the amygdala is very quick, a direct connection, but not very precise, because most of the sensory information goes via the other path, up to neocortex, where it is analysed through several circuits while a response is formulated. But the amygdala, meanwhile assesses the sensory data to see if it has emotional meaning and can trigger a response while the neocortex is still sorting things out. Emotions may be very difficult to control because the amygdala turns on other parts of the brain before the thinking brain, the neocortex does. Because the amygdala has diverse connection to parts of the brain that control the autonomic nervous system, as well as connections to the cortex, which is responsible for conscious experience, there is a convergence, giving it a central role in emotional life, so it can mobilize the body to respond with a strong emotion, particularly fear, before the thinking brain quite knows what is happening. Scientist have discovered that there is an anatomical connection between the frontal cortex and the amygdala. From recent experiments, it appears that one important function of this connection is for the frontal cortex to regulate or turn off the amygdala.