It is true that a healthy vagina, and particularly uterus, plays an important role in embryo implantation and success in IVF. The condition of the vagina can be assessed through a clinical test and secretion culture of both from the vagina and the ectocervix (vaginal part of the cervix). This test should not though be taken during the period as it lessens its reliability. On the other hand, an evaluation of the state of the uterus requires more specialized tests. Firstly an ultrasound check will assess the texture and morphology of the uterus. Also an endometrial culture can be done, except it must not derive from period material. I would suggest that you do a biopsy at a specialised centre a few days after the end of the period. Thus, should any microbes be found in the uterus, they can be dealt with.
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