Hormone abnormalities other than PCOS can also lead to irregular menstrual cycles. Such abnormalities include problems with the thyroid gland (which produces a hormone that controls metabolism), abnormal levels of prolactin (a hormone that induces breast milk production), and a lack of hypothalamic/pituitary stimulation to the ovary known as functional hypothalamic amenorrhea (FHA). The pituitary gland has been called the master gland of the body; it secretes hormones that control a wide range of functions, including reproduction, metabolism, response to stress, water balance, and growth.

Women with irregular cycles should have both their thyroid hormone and prolactin levels measured, as problems with the thyroid gland can indirectly lead to elevations in prolactin. Low levels of thyroid hormone (hypothyroidism) and elevations in prolactin (hyperprolactinemia) can be readily treated with medication. In fact, treatment of hypothyroidism with oral thyroid hormone (levothyroxine) can promptly restore normal menstruation. Similarly, hyperprolactinemia usually responds quickly to bromocriptine therapy, often promptly restoring normal cycles.

An elevation of prolactin in the absence of any thyroid disease requires magnetic resonance imaging (MRI) of the brain to evaluate its cause. In such cases, hyperprolactinemia usually results from an increased growth of the prolactin-secreting cells in the pituitary gland forming a small tumor. If the prolactin-secreting tumor is less than 1 cm in diameter, then it is called a microadenoma, whereas a macroadenoma is greater than 1 cm in diameter. These are not life-threatening conditions and usually respond very well to medication, which is well tolerated with few side effects.

Women without thyroid or prolactin issues, and with low or normal FSH levels, who fail to have menstrual periods following treatment with progesterone are usually referred to as having functional hypothalamic amenorrhea (FHA). These women demonstrate no follicle growth and therefore fail to produce normal levels of estrogen despite an appropriate complement of ovarian follicles. Women who are below ideal body weight and who exercise frequently and vigorously are particularly prone to developing this problem. Women with FHA are at risk for osteoporosis and should discuss with their physician the benefits of hormone therapy (such as oral contraceptives) when not attempting pregnancy. They should also undergo an MRI of the brain to rule out any structural etiology for their condition. Women who are below ideal body weight may resume normal menstrual cycles when they gain weight or decrease their exercise frequency and duration.

Infertility in women with FHA can be readily treated with injectable gonadotropins. In such women, the choice of medication is important as the drug should contain both FSH and LH (Menopur) and not just FSH alone (Gonal-F, Follistim). Clomid rarely works in women with FHA, but nearly all women with FHA can undergo successful ovulation induction. As was discussed in the preceding question, an excessive response may lead to high order multiple pregnancy, so care should be taken to cancel such a cycle or convert it to IVF or consider a follicle reduction procedure.