Circadian rhythms are regular changes in mental and physical characteristics that occur in the course of a day (circadian is Latin for around a day). Most circadian rhythms are controlled by the body's biological clock. This clock, called the suprachiasmatic nucleus or SCN, is actually a pair of pinhead-sized brain structures that together contain about 20,000 neurons. The SCN rests in a part of the brain called the hypothalamus, just above the point where the optic nerves cross. Light that reaches photoreceptors in the retina (a tissue at the back of the eye) creates signals that travel along the optic nerve to the SCN.

Signals from the SCN travel to several brain regions, including the pineal gland, which responds to light-induced signals by switching off production of the hormone melatonin. The body's level of melatonin normally increases after darkness falls, making people feel drowsy. The SCN also governs functions that are synchronized with the sleep/wake cycle, including body temperature, hormone secretion, urine production, and changes in blood pressure.

By depriving people of light and other external time cues, scientists have learned that most people's biological clocks work on a 25-hour cycle rather than a 24-hour one. But because sunlight or other bright lights can reset the SCN, our biological cycles normally follow the 24-hour cycle of the sun, rather than our innate cycle. Circadian rhythms can be affected to some degree by almost any kind of external time cue, such as the beeping of your alarm clock, the clatter of a garbage truck, or the timing of your meals. Scientists call external time cues zeitgebers (German for time givers).

When travelers pass from one time zone to another, they suffer from disrupted circadian rhythms, an uncomfortable feeling known as jet lag. For instance, if you travel from California to New York, you lose 3 hours according to your body's clock. You will feel tired when the alarm rings at 8 a.m. the next morning because, according to your body's clock, it is still 5 a.m. It usually takes several days for your body's cycles to adjust to the new time.

To reduce the effects of jet lag, some doctors try to manipulate the biological clock with a technique called light therapy. They expose people to special lights, many times brighter than ordinary household light, for several hours near the time the subjects want to wake up. This helps them reset their biological clocks and adjust to a new time zone.

Symptoms much like jet lag are common in people who work nights or who perform shift work. Because these people's work schedules are at odds with powerful sleep-regulating cues like sunlight, they often become uncontrollably drowsy during work, and they may suffer insomnia or other problems when they try to sleep. Shift workers have an increased risk of heart problems, digestive disturbances, and emotional and mental problems, all of which may be related to their sleeping problems. The number and severity of workplace accidents also tend to increase during the night shift. Major industrial accidents attributed partly to errors made by fatigued night-shift workers include the Exxon Valdez oil spill and the Three Mile Island and Chernobyl nuclear power plant accidents. One study also found that medical interns working on the night shift are twice as likely as others to misinterpret hospital test records, which could endanger their patients. It may be possible to reduce shift-related fatigue by using bright lights in the workplace, minimizing shift changes, and taking scheduled naps.

Many people with total blindness experience life-long sleeping problems because their retinas are unable to detect light. These people have a kind of permanent jet lag and periodic insomnia because their circadian rhythms follow their innate cycle rather than a 24-hour one. Daily supplements of melatonin may improve night-time sleep for such patients. However, since the high doses of melatonin found in most supplements can build up in the body, long-term use of this substance may create new problems. Because the potential side effects of melatonin supplements are still largely unknown, most experts discourage melatonin use by the general public.