Temperature--Your temperature is lowest when you're inactive. And activity can make your temperature rise. But despite these factors, your temperature also follows a definite circadian rhythm.

In the late afternoon, your temperature can be as much as 2 degrees Fahrenheit higher than in the morning. And it will rise and fall even if you never see daylight. 
Hormone production--Almost all hormones are regulated, to some extent, by circadian rhythms.

Cortisol affects many body functions, including metabolism and regulation of your immune system. Its levels are highest between 6 and 8 a.m. and gradually decline throughout the day. If you change your daily sleeping schedule, the peak of cortisol's cycle changes accordingly.

Growth hormones stimulate growth in children and help maintain muscle and connective tissue in adults. Sleep triggers hormone production, regardless of when you go to bed. Production peaks during the first two hours of sleep. If you're sleep deprived, production drops.

Cardiovascular system--More strokes and heart attacks occur in the morning than at any other time of day. This makes some people wonder if morning exercise is safe.

But experts contend morning changes in your body--not exercise-- may be responsible for cardiovascular problems. Blood clots most rapidly at about 8 a.m.

Blood pressure also rises in the morning and stays elevated until late afternoon. Then it drops off and hits its lowest point during the night.

These changes occur independently of physical activity. Exercise at any time of the day is beneficial.

On the other hand, if you're training for athletic competition, you may have reason to schedule that event later in the day. Athletes seem to perform best in the late afternoon, when strength, body temperature and flexibility peak.

Pain tolerance--Athletes who compete late in the day may perform better because they can "gain" without as much "pain." Pain tolerance is highest in the afternoon. One study shows tooth pain is lowest in the late afternoon, a consideration when you schedule your next dental appointment.

Medication--Scientists are looking at how circadian rhythms affect the way your body uses medications. One finding is that less anesthesia is needed to cause analgesia or drowsiness when administered in the afternoon.

Experiments with cancer medications are trying to find the time of day when the drugs are the most helpful with the fewest side effects.

Sex --The majority of sexual encounters took place at bedtime (11 pm to 1 am). The most common explanations for this temporal pattern is the biological clock has a time set for sexual arousal.

Heart attacks--The chances of suffering heart problems are not equal throughout the day. Heart attacks occur more often around 10 o'clock in the morning than any other time, a peak that previously was attributed to daily behavior patterns getting underway
Stay on schedule

Changes in daily habits such as a short night's sleep can disrupt your circadian rhythms. You may be able to stay "in sync" by keeping a consistent daily schedule.

Blind:

Most totally blind people have circadian rhythms that are "free-running" (i.e., that are not synchronized to environmental time cues and that oscillate on a cycle slightly longer than 24 hours). This condition causes recurrent insomnia and daytime sleepiness when the rhythms drift out of phase with the normal 24-hour cycle.10-mg dose of melatonin was given daily one hour before bedtime will achive a normal ryththm.. The dose was then reduced to 0.5 mg per day over a period of three months; the entrainment persisted, even at the lowest dose.

Circadian rhythms are internal body clock cycles which control 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").