Increasing evidences derived from experimental and clinical studiessuggest that the hypothalamo- pituitary- thyroid axis and hypothalamo- pituitary ovarian axis are physiologically related to act together. Both hyper and hypothyroidism may result in menstrual disturbances. Treatment of young infertile women and women with menstrual cycle dysfunctions by thyroid hormones led to improvement of the cycle and frequently also desired conception by direct effect of TSH, and T3 on steroidogenesis and oocyte maturation. Hypothyroidism is often associated with ovarian follicular cysts, and hypogonadism. It is useful to investigate the intraovarian changes that lead to development of ovarian cyst in response to gonadotropin treatment.