to Getpregnantblog.com 
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Apart from poor endometrial receptivity which I wrote about in a previous article apparently there are other factors which can affect the quality of the lining.
As most women trying to conceive a baby know, estrogen and progesterone are critical factors in uterine lining and implantation. Adequate estrogen is required early in the cycle to ensure that the lining grows to the right thickness and quality. This is because estrogen triggers endometrial cells in the lining of the uterine to divide and prolierate. Progesterone stops this proliferation (after ovulation) and helps the lining to become a stable place for the egg to implant.
During Assisted Reproduction Techniques (ART), like IVF, and sometimes even IUI women are often put on estrogen and/or progesterone at different times during their cycle. It turns out that the doses and method of administration of these drugs can make a huge difference to the quality of the lining.
Vaginal administration promotes an uterine lining that has a more normal structure, and is thus more conducive to successful implantation than intramuscular administration. So be sure to ask your doc about this and if possible request the vaginal administration.
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