There is as such no exact duration for medications used in IVF injections. It depends case to case and complexity and severity of cases that how many days are required for IVF injections. Side effects or risks associated with IVF injections can be miscarriages in the case of ectopic pregnancy, multiple births, and side effects of fertility medications.
If you have low levels of hypothyroidism, then in this case you may not ovulate. You can cover the lack of hormone in your body by taking the right dose of thyroxine as well as you can restore your fertility. You may have also found that your underactive thyroid is a reason of not getting a positive pregnancy.
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