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Christine, I wrote a college term paper on this topic for a Sportsmedicine and Exercise Physiology class. I recall it's the estrogen hormone that is not produced in normal amounts when a woman stops menstruating.
I suggest discussing your condition with your doctor to see if anything needs to be done to help the process along.
When estrogen isn't being produced in sufficient quantities, this can lead to decreased calcium levels in your bones and to osteoporosis, which often leads to stress fractures.
This is often due to high levels of training and a restricted caloric intake.
When I ran cross-country in college, there were several runners who were borderline anorexics and were not menstruating. The long term effects of this cannot be good. Unfortunately some of these women were good runners, so this created a mimicking effect with the less talented runners...
When I say "borderline" they are not like the anorexics you often see on TV who eat celery and carrot sticks and have total caloric counts per day of under 600 calories. These are active women who choose to eat salad instead of pasta after a hard workout, and their caloric intake per day may be closer to 1000 to 1200.
However simply having your menstrual cycle doesn't mean you weigh too much. I'm 5'4 and 100 pounds and I have regular cycles. It varies with the individual I think. But at least I know my bones are healthy because I eat a balanced and healthy diet
Regarding eating more on days you run vs. days off... I find that I eat more in the day or 2 after I've done a hard workout. Sometimes it takes that long for my body to know that it needs more food than it is getting. I run in the mornings, and find it hard to eat right after running, and usually for hours afterwards.
Everyone's different so whatever works for you should be fine as long as you listen to what your body is telling you. Your food cravings are often a sign of what your body needs (but not always).
Good luck!
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