Hypothalamic Amenorrhea: a common cause of missing periods

We see many women in our practice who have long menstrual cycles, or are skipping cycles completely. This often happens as a result of the metabolic and hormonal imbalance seen in PCOS. That said, PCOS is just one cause of long cycles or missing periods. Another common cause that isn’t commonly discussed is Hypothalamic Amenorrhea (HA).

What is Hypothalamic Amenorrhea?

Hypothalamic Amenorrhea refers to a loss of the menstrual cycle for several months due to problems arising from the brain region called the hypothalamus. This area sits in the base of the brain near the pituitary gland. Most importantly, it plays an essential role in hormone production.

The hypothalamus produces a hormone called GnRH (gonadotropin-releasing hormone), which tells the pituitary gland to produce two hormones: LH and FSH. These two hormones then signal the ovaries to produce estrogen and mature eggs for ovulation, which leads to a menstrual cycle.

In the case of Hypothalamic Amenorrhea, the signal from the brain—initiated in the hypothalamus—is disrupted. As a result, this hormone production cycle is interrupted, and women stop cycling regularly.

Hypothalamic Amenorrhea can be caused by stress

What Causes Hypothalamic Amenorrhea?

There are several causes of Hypothalamic Amenorrhea. Some of the most common include: excessive exercise, elevated chronic stress, and restrictive eating patterns.

In all three of these cases, the body is under increased emotional or physical stress. As a result, it determines that it’s not in the body’s best interest to spend valuable resources ovulating and potentially getting pregnant.

In this sense, HA can be thought of as the incredibly intelligent body’s “self-preservation” technique. The body stops the GnRH production from the hypothalamus, the pituitary doesn’t receive the signal to produce LH and FSH, and the ovaries don’t receive messages to ovulate.

How do you know if it’s Hypothalamic Amenorrhea?

Hypothalamic Amenorrhea isn’t the only cause of missing or long cycles. As a result, if it isn’t clear based on your history, some simple blood tests can indicate if you have HA. I typically start by running the following three hormones:




Low levels of all three are indicative of HA, whereas elevated LH in comparison to FSH is more indicative of PCOS.

Alleviate Hypothalamic Amenorrhea with Yoga


If you’ve been diagnosed with HA, then treatment should focus on your individual cause(s). If you’re extremely stressed, then choose stress management techniques such as meditation and yoga. Prioritize proper sleep and a healthy, nourishing diet. These are essential to getting better. You can also utilize acupuncture and certain botanicals for additional support.

If the cause of your HA is excessive exercise, you may need to put a foot on the brake pedal for a little while. Try more calming, nourishing activities instead.

If your HA is related to restrictive eating patterns, then expand your diet to get your cycle back. Many women try ketogenic diets and end up losing their cycle as a result.

No matter what the cause, the goal is to send messages to your body that you’re safe, and well nourished.

Key Takeaways

  • Hypothalamic Amenorrhea is one of several potential causes of long or missing cycles
  • Common causes of HA are intense chronic stress, restrictive eating patterns, and excessive exercise
  • If you’re not sure whether HA is the cause of your missing cycles, running three blood hormone levels can give you some important information: LH, FSH, Estradiol

Next Steps

If you have long or missing menstrual cycles and don’t know why, consider testing the hormones listed above to get more information.

And of course, if you’re in Ontario or the greater Toronto area and are ready to get a naturopathic perspective, you can book an appointment with one of our Naturopathic Doctors at the White Lotus clinic here.