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Usually on days 3-7, or 4-8, or 5-9 of your cycle. Depending on your doctor. It does not matter how long your period last, you will take the pills starting on day 3, 4, or 5 and will take it for 5 days. So if the doc prescribes you 5 pills it will be 1 each day, if he prescribes 10 it will be 2 each day. If you take more than 1 per day you take them at the same time. Usually you will start out with 1 per day and if you are not successful, than the doc will up the dosage.
Day one of your menstrual cycle is the first day of full flow. Your doctor will prescribe the med's for you and will tell you what he thinks is the best day for you to begin taking it. I took Clomid for 5 cycles and always on days 3-7, but the norm is days 5-9. There is research for both instances with positives and negatives.
When I was on Clomid I would go in to the office on day 12 of my cycle for an ultrasound to see if I had any follicles, and what size they were. From that the doctor would predict when I was likely to ovulate. In a perfect scenario you would ovulate on day 14. So you should be having intercourse about every other day (so the sperm has time to re supply) starting on day 9 or 10 of your cycle until day 17-18 just to be sure you are not missing the window of opportunity.