Functional Hypothalamic Amenorrhea – When the Body Intentionally Switches Off the Cycle

Woman at a consultation in a private medical clinic with a doctor
This material was prepared by a gynecologist. The text is based on clinical practice and current international guidelines for the management of functional hypothalamic amenorrhea and menstrual cycle disorders.

Sometimes menstruation disappears not because the body has “broken down”.
But because it has chosen a pause.

In recent years, I increasingly see women aged 25–40 who come with the same question: “My cycle has stopped. Is this forever?”

No surgeries.
No oncology.
No genetic diagnoses.

But a different reality.
Chronic tension.
Relocations.
Work without breaks.
Weight control.
Fragmented sleep.

Functional hypothalamic amenorrhea often frightens more than many diagnoses. Because it looks unclear.
And because it is frequently confused.

In this article, I will explain FHA the way I do during consultations.
Calmly.
Directly.
To the point.

What functional hypothalamic amenorrhea really is

Functional hypothalamic amenorrhea is the absence of menstruation that occurs not due to ovarian disease.

This is important.

It is not:

  • a hormonal breakdown
  • ovarian exhaustion
  • the onset of early menopause

In FHA, the ovaries are most often anatomically preserved. Follicles are present. Ovarian reserve may be normal.
But the cycle is switched off.
Why?

Because the reproductive system is controlled from above. And the decision is made there.

FHA is a regulatory, protective mechanism. Not a defect. Not a diagnosis of “impossibility”.

It is the body’s response to conditions it perceives as unsafe.

Why the body “switches off” the menstrual cycle

The menstrual cycle is not a vital function. It is a luxury. The body maintains it only when it is confident that resources are sufficient.

When resources are lacking – it economizes.
Without emotions.
Without drama.
Without warnings.

Stress as the main triggering mechanism

This is not about “being nervous for a couple of days”. This is about chronic tension that becomes the background of life.
Job loss.
Relocation.
Loss of a sense of safety.
Responsibility without support.
Constant control.

At the physiological level, it looks like this:

  • cortisol remains chronically elevated
  • the hypothalamus reduces GnRH pulses
  • FSH and LH decrease
  • ovulation is switched off

Not because the body “failed”.
But because it chose survival.

The main conductor is the hypothalamus, not the ovaries

The menstrual cycle does not start in the ovaries. It begins in the hypothalamus.

The hypothalamus does not evaluate lab results. It evaluates the environment.

If living conditions appear unfavorable, the hypothalamus reduces impulses that initiate the entire chain:

  • hypothalamus
  • pituitary gland
  • ovaries

As a result:

  • FSH and LH decrease
  • ovulation does not occur
  • estrogen levels fall
  • the cycle disappears

The ovaries are not “to blame” here. They simply do not receive the command.

Energy deficit, stress, and survival

In real life, this almost never looks like a single factor. More often, it is a scenario.

Chronic stress.
Sleep deprivation.
Dietary restrictions.
High physical load.
Control.
Lack of recovery.

The body perceives this as a survival state. And in survival mode, reproduction is not a priority.
No esoterics.
Pure biology.

How FHA looks in real life, not in textbooks

A typical patient profile I see in practice

Most often, this is a woman aged 25–40.
Smart. Responsible. Used to “keeping everything under control”.

She works a lot. Trains frequently. Rarely rests.
She is demanding toward her body. Harsh toward herself.

These women most often miss the early signals. Until the cycle disappears completely.

Symptoms most often mistaken for a “hormonal imbalance”

FHA rarely starts abruptly. Usually, the first signs are:

  • cycle lengthening
  • loss of ovulation
  • scant menstruation
  • instability from month to month

Later:

  • complete absence of menstruation
  • mucosal dryness
  • decreased libido
  • increased fatigue

Subjectively, this is easily mistaken for a “hormonal imbalance”. Or for the onset of menopause.

FHA and early menopause – why they are so often confused

The fundamental difference between these conditions

The difference is fundamental.

  • FHA is reversible
  • early menopause is not

In FHA:

  • the reserve is preserved
  • regulation is switched off
  • the prognosis is good if conditions change

In early menopause:

  • the reserve is depleted
  • follicles do not return
  • the management strategy is different

Why sensations do not help distinguish one from the other

Because symptoms can be similar.

Hot flashes. Dryness. Absence of a cycle.

By sensations alone, it is impossible to tell.
Only numbers and the logic of interpretation make the distinction.

What happens to hormones in functional amenorrhea

FSH, LH, and estradiol – the typical FHA pattern

Most often, we see:

  • FSH – low or at the lower limit of normal
  • LH – reduced
  • estradiol – low

This is not depletion. It is the absence of a signal.

AMH in FHA – what matters and what it does not show

AMH in FHA is most often:

  • normal
  • or moderately reduced

It does not “drop forever because of stress”. AMH reflects reserve, not the current functioning of the cycle.

This is exactly why FHA is so often confused with more serious conditions.

How clinicians distinguish FHA from other causes of amenorrhea

Why one test is not enough

Because hormones function as a system. One parameter without context means nothing. What matters is:

  • how hormones look as a whole
  • what ultrasound shows
  • what is happening with the body and lifestyle

Which examinations actually make sense

As a rule, it is sufficient to assess:

  • FSH, LH, estradiol
  • AMH
  • pelvic ultrasound
  • the clinical context

Checklists do not work here. Clinical reasoning does.

Clinical example

Patient, 29 years old.
A year of intensive work. Training 5 times per week. Diet “under control”.

No menstruation for 4 months.

FSH – 3.8.
Estradiol – reduced.
AMH – 2.3.
Ultrasound – follicles preserved.

After restoring sleep, reducing load, and eating without deficit, the cycle returned after 3 months.
No hormonal therapy.
This is FHA.

Is functional hypothalamic amenorrhea treatable

Why “just giving hormones” is a bad idea

Hormones can induce bleeding. But they do not restore regulation.

This creates an illusion of a solution. While the problem remains.

What actually helps restore the cycle

It is not a pill that works.

Conditions do:

  • sleep
  • adequate nutrition without deficit
  • reduction of chronic stress
  • reassessment of physical load

This is not lifestyle advice. This is endocrinology.

When FHA requires timely medical attention

Functional hypothalamic amenorrhea is reversible. But not indefinitely.

There are situations where waiting is dangerous:

  • amenorrhea longer than 6 months
  • signs of pronounced estrogen deficiency
  • reduced bone density
  • pregnancy planning

In these cases, a “wait and see” approach may come at too high a cost.

Frequently asked questions

Is FHA dangerous?

With prolonged duration – yes. Especially for bone health.

Does FHA affect fertility?

While the cycle is off – yes. After recovery – no.

Can FHA turn into menopause?

No. These are different processes.

Will the cycle recover?

In most cases – yes, if conditions change.

Conclusion

Functional hypothalamic amenorrhea is not a verdict. But it is not trivial either.
It is a signal.

A signal that the body is living in a mode it perceives as unsafe.

And the most common clinical question here is not “what to treat it with”, but: WHAT in the patient’s life is being pushed to the limit and WHERE the body is no longer coping?

The cycle returns not because of words. It returns because of conditions.
And yes – sometimes this requires decisions. Not only medical ones.

But this is exactly what mature, honest medicine looks like.

Clinical guidelines and sources

  1. Endocrine Society. Functional Hypothalamic Amenorrhea: An Endocrine Society Clinical Practice Guideline. 2017.
  2. Gordon C.M., Ackerman K.E., Berga S.L. et al. Functional Hypothalamic Amenorrhea: An Endocrine Society Clinical Practice Guideline. Journal of Clinical Endocrinology & Metabolism, 2017.
  3. ESHRE. Guideline on the management of women with hypothalamic amenorrhea. Updated clinical guidance.
  4. Warren M.P., Chua A.T. Exercise-induced amenorrhea and bone health in the adolescent athlete. Annals of the New York Academy of Sciences.
Dr. Lyudmila Shpura
Obstetrician-gynecologist
More than 14 years of practical experience
New Life Medical Center
2026