Hypothalamic amenorrhoea

Hypothalamic Amenorrhoea

Hypothalamic amenorrhoea is the medical name for when regular menstrual bleeding stops due to the influence of the hypothalamus and the hypothalamic-pituitary-adrenal (HPA) axis.​1​

The hypothalamus releases hormones, regulates body temperature, and other important system tasks.

Amenorrhoea is the medical name for the absence of menstrual periods. Thus, hypothalamic amenorrhoea refers to a lack of menstrual bleeding due to influences on the action of the hypothalamus.

Causes of hypothalamic amenorrhoea

  • Low body fat due to exercising or disordered eating​2​, extreme dieting or a lack of carbohydrates in the diet​3,4​
  • Chronic stress, consistently elevated cortisol levels​5​
  • Pituitary gland tumour or other growth
  • Hypothyroidism​6​

The mixture of disordered eating, osteoporosis, and the loss of periods was first described in 1997 and was nicknamed the ‘female athlete triad’.

Why is the hypothalamus important for menstruation?

The hypothalamus controls fertility by producing one specific hormone that triggers the rest of the menstrual cycle: gonadotropin-releasing hormone (GnRH).​5​

GnRH sends signals for the production of leutinising hormone (LH) and follicle-stimulating hormone (FSH), stimulating the ovaries to produce oestrogen, testosterone and some progesterone.

The female reproductive system cycle doesn’t function well without these hormones, causing many system-wide impacts.

Symptoms of hypothalamic amenorrhoea

  • Absence of menstrual bleeding for long stretches
  • Scanty, irregular periods
  • Increased vaginal microbiota disturbances such as bacterial vaginosis (BV) and aerobic vaginitis (AV) (low oestrogen, low glycogen, low lactobacilli)
  • Low sex drive (low overall hormone levels)
  • Dry, irritated vagina (lack of oestrogen)
  • Low oestrogen signs (ovaries not receiving the signal to produce oestrogen)
  • Low progesterone signs (not ovulating, so no progesterone is produced)
  • Mood changes – irritability, anxiety
  • Appetite changes
  • Gut microbiota disturbances​7​and subsequent digestive symptoms
  • Insomnia (low progesterone, possibly low carb intake)
  • Feeling cold
  • Infertility
  • Low thyroid function and associated symptoms​6,8​
  • Later in life, due to a lack of oestrogen for long periods of time, bone density loss and osteoporosis are a factor

Why low body fat and high cortisol stop periods

You may have noticed that many of the reasons for periods stopping involve high cortisol levels.​9​

Cortisol is a stress hormone, and while it’s not the only reason for periods to be interrupted, it is a major blockade to normal hormone function.

Cortisol is a sign of stress; if periods are skipped, cortisol may be elevated chronically.

Another signal may be caloric stress (not enough calories or carbs available, like during famine), or that you are physically extremely active. High cortisol could also be caused by adrenal or pituitary tumours or other dysfunction.

Not having enough body fat to produce the needed hormones can also disrupt a normal menstrual cycle. This is why tall, slim girls get their periods later than everyone else.

If you follow a low-calorie, low-fat diet and have a low body mass index (BMI), exercise a lot (and have low body fat), or are chronically stressed, you may have a clearer answer to a loss of periods.

Diagnosing hypothalamic amenorrhoea

There is a process of elimination, considering other causes of a loss of periods, including pregnancy or other health conditions before a diagnosis can occur.

Hormone blood tests

  • Follicle-stimulating hormone (FSH)
  • Luteinising hormone (LH)
  • Prolactin (for pituitary tumours)
  • Human chorionic gonadotropin (hCG) (for pregnancy)
  • Cortisol
  • Adrenocorticotropic hormone (ACTH) (regulates cortisol production)

What is the ‘progesterone challenge?’

You may undergo the ‘progesterone challenge’, which involves the administration of progesterone to attempt to induce menstrual bleeding.

If you have hypothalamic amenorrhoea, you will not bleed during this test because the signal for your ovaries to produce oestrogen is absent. Thus, the endometrial lining will be thin or absent.

Brain scans and blood tests

You may have a brain scan to check for tumours or other abnormalities of the pituitary, hypothalamus or adrenal glands.

Treating hypothalamic amenorrhoea

You might think it’s fun or convenient to skip your periods for a while, but a regular period is a sign of good health in women. When periods stop or become irregular, it means something is up and needs your attention.

Treatment will depend heavily on the cause. There may be obvious causes of lost periods, like being underweight, so interventions may be prescribed to improve this first.​4​

Treatments may include:

  • Increase body fat (you need fat to make oestrogen)
  • Increase intake of calories and possibly carbohydrates (you need calories and carbs to ease stress hormone – cortisol – production)
  • Do less exercise or less vigorous exercise
  • Herbal medicines
  • Supplements
  • Hormones or medications
  • Psychological therapy
  • If a tumour is implicated, your doctor will discuss your options with you

The goal of any treatment is to first assess for more serious issues and then correct the underlying imbalance. It’s important to see your doctor for thorough assessments to rule out pituitary tumours or other serious causes.

Assessing body fat percentage

Body fat is the first port of call – if you have less than 17% body fat, your body can’t produce enough oestrogen to start the hormonal cycle. If you exercise a lot, low body fat can be an issue.

It might be hard to consider putting on weight or dropping down your exercise regime but remember that your bone health and healthy hormones do way more for your well-being, libido, and happiness than you could ever imagine being super fit or fat-free would do.​10​

High cortisol levels

If you are chronically stressed, your cortisol blocks the brain from sending out strong enough fertility signals while also inhibiting many body processes, such as immunity.

Typically, the thyroid is one of the first things affected by high cortisol levels.

If you are stressed, find support and learn some strategies to help. Luckily, most of these are free. If you aren’t sure, get a full assessment from your doctor, including a full cortisol test.

If you have high cortisol, it’s possible that other hormones involving the adrenal glands need to be assessed.

Why a lack of menstruation isn’t a disease by itself

It’s important to remember that hypothalamic amenorrhoea is the medical name for your periods stopping specifically due to the hormonal cascade in the brain being interrupted.

Hypothalamic amenorrhoea is not a disease in and of itself but a symptom.

How the hypothalamus regulates your fertility

The hypothalamus is the area of your brain responsible for controlling your fertility due to the one important hormone it produces, GnRH.

Gonadotropin-releasing hormone (GnRH) is the hormone that gets sent into your body and brain that signals for the production of other hormones required both before and after ovulation: follicle-stimulating hormone (FSH) and luteinising hormone (LH), respectively. (Which is why they are part of the testing regime.)

These two hormones, in turn, stimulate oestrogen production, which impacts cervical mucous, and progesterone, which prepares the uterine lining for a fertilised egg.

Once the hypothalamus stops producing GnRH, all other hormones, in turn, stop being produced, bringing your menstrual cycle and fertility to a grinding halt or being stop-start if signals are patchy.​11​

Understanding medical terms

The classifications matter because the cause can be narrowed down a little easier if you know whether periods used to be normal and then something changed, or, if they were never normal. This is an important clue.

Primary = from the beginning, first
Secondary = appeared later, second

(From Greek)
a – negative
men – month
rhoia – flow

Never had a period (primary amenorrhoea)

If you have never had a period, it is known as primary amenorrhoea, because the interruption to a normal menstrual cycle was there from birth or puberty. ​12​

Hypothalamic amenorrhoea can fit into the primary amenorrhoea category for the same reasons as it fits into the secondary classification: stress, disordered eating, and over-exercising.

Young girls are more stressed than ever, and interruptions to brain chemistry and hormone systems can occur around the time periods would normally be starting.

Period started then stopped (secondary amenorrhoea)

When your period stops after being regular or at least present (but maybe irregular), it is medically known as secondary amenorrhoea.

Not getting a period for a while or skipping periods means something has changed, and the cause of that change needs to be investigated. Something is going awry.

Find more options for cause of periods stopping on the secondary amenorrhoea page


  1. 1.
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Josephine Cabrall BHSc(NAT) | ATMS
Josephine Cabrall is qualified naturopath specialising in PCOS and hormonal and fertility issues, based out of Melbourne, Australia. Josephine is a fully insured member of the Australian Traditional Medicine Society (ATMS).