The speeding up and slowing down activity characteristic of the stress response is controlled by a gland in your brain called the hypothalamus. The main job of the hypothalamus is to maintain the homeostasis (i.e., the set-point) of important body systems including blood pressure, body temperature, fluid balance, body weight, sexual activity, sleep/wakefulness, and emotions. The hypothalamus is like a thermostat that receives inputs from other parts of the brain and body about the body's internal environment. If body functions are out of balance, the hypothalamus sends messages to the ANS and to the pituitary gland to speed up or slow down relevant glands and organs to bring the body back into balance at the set-point appropriate to each system. The pituitary gland, sometimes referred to as the 'master gland', secretes hormones that are responsible for the regulation of all other endocrine glands (glands that secrete hormones directly into the blood) in the body.
Some of the hormones secreted by the hypothalamus and pituitary gland stimulate the limbic system, a complex collection of sub-cortical brain structures that control emotions, motivation, and the formation of long-term memories. The limbic system is heavily interconnected with the brain's frontal cortex, which is the part of the brain that controls judgment, attention, and decision-making. The limbic system and the frontal lobes work together to make possible the appraisals or judgments regarding whether or not a stressor is dangerous or exceeds our coping ability that were described above in the section concerning Stage 2. The combined limbic/frontal system also influences whether we fight, flee, or freeze in the presence of a stressor.