Pregnant, or Just Underfed?The Science Behind Hypothalamic Amenorrhea

Missing a period often raises one big question: Am I pregnant? But for many young women—especially athletes, those under chronic stress, or individuals with restrictive eating habits—the real answer may lie elsewhere. 

Hypothalamic Amenorrhea (Functional Hypothalamic Amenorrhea or FHA) is a condition where the brain halts the menstrual cycle, because it senses that the body is under too much stress, or running on too little fuel. While not having your period might sound like a dream come true, the consequences of FHA are far from harmless. This article explores the science at work behind FHA, its root causes, the health risks it poses, and how it can be reversed.

What is Hypothalamic Amenorrhea?

Amenorrhea refers to the absence of menstruation, and namely, there are two types:

1. Primary amenorrhea: When menstruation hasn’t started by age 16, or within five years after the onset of puberty.

2. Secondary amenorrhea: When someone who previously had regular periods stops menstruating for three months or more. 

Hypothalamic amenorrhea falls into the second category, and as the name suggests, is caused by disruptions in the hypothalamus—a key regulatory centre located deep within the brain. The hypothalamus is responsible for regulating many bodily processes, including reproduction.

The HPO and HPA Axes

In a healthy menstrual cycle, the hypothalamus-pituitary-ovarian (HPO) axis as can be seen in the diagram above, is responsible for regulating reproductive activity—coordinating hormonal signalling between the brain and the ovaries. The process, is as follows:

1. The hypothalamus releases gonadotropin-releasing hormones (GnRH) in a pulsatile manner.

2. GnRH signals the anterior pituitary gland to release luteinising hormone (LH) and follicle-stimulating hormone (FSH).

3. Together, LH and FSH stimulate the ovaries to produce oestrogen and mature ovarian follicles—eventually leading to ovulation.

4. If no pregnancy occurs, menstruation takes place.

However, in hypothalamic amenorrhea, this entire cascade is disrupted at the very first step. Under physiological or psychological stress, the hypothalamus reduces or halts GnRH secretion. Without GnRH, the pituitary gland is unable to release LH and FSH, resulting in low oestrogen levels, anovulation, and the menstrual cycle being put on pause.

Also at play is the hypothalamic-pituitary-adrenal (HPA) axis, which governs the body’s stress response. When the brain perceives prolonged threat, whether that be physical (e.g. starvation, overtraining) or emotional (e.g. emotional distress), the HPA axis is activated—the adrenal glands release cortisol, the body’s primary stress hormone. Chronically elevated cortisol levels have a suppressive effect on the HPO axis; it interferes with GnRH secretion, which in turn disrupts the whole cascade of events that follow. In other words, when your body feels unsafe, it conserves energy by shutting down fertility.

What Causes Hypothalamic Amenorrhea?

FHA can be triggered by one, or a combination of the following:

• Low energy availability from under-eating, excessive exercise, or both

• Prolonged periods of psychological or physical stress

• Low body fat percentage

• Sudden and/or excessive weight loss

Though often under and misdiagnosed, FHA is more common than we think—affecting an estimated 1.62 million women aged 18-44 in the US and 17.4 million worldwide, according to the Cleveland Clinic. It is most commonly observed however, among athletes, especially those who have intense training regimes, individuals with restrictive eating disorders like anorexia nervosa and bulimia, but also people under chronic stress.

Why It Matters: The Consequences of FHA

While the most obvious consequence is by definition, an absence of menstruation, FHA poses a wide range of health risks due to chronically low estrogen and hormonal imbalances. These can include:

• Poor bone health, bone density loss—increasing the risk of early-onset osteoporosis

• Infertility

• Mood changes, higher susceptibility to mental disorders such as anxiety or depression

• Fatigue and low energy

• Cold intolerance

• Skin and hair issues such as hair loss and acne

• Increased risk of cardiovascular disease

• Low libido

Can Hypothalamic Amenorrhea Be Reversed?

It is possible to reverse FHA—but it requires addressing the root causes at play. FHA is more so a symptom of a larger, underlying physical or psychological problem, rather than a stand-alone health complication. 

Evidence-based recovery strategies include:

• Increasing energy intake, especially carbohydrates and fats

• Reducing high-intensity exercise or taking a complete break from exercise

• Restoring healthy body fat levels and weight gain 

• Managing psychological stress

Some people turn to birth control pills or hormone treatment to artificially induce their periods, but this often acts as a band-aid solution. While it may cause withdrawal bleeding, it does not restore natural hormonal function or reverse the consequences caused by FHA. 

In short, hypothalamic amenorrhea is the body’s way of letting you know that you aren’t at optimal health. In a culture where diet obsession and overachievement are often glorified, many individuals fall into energy deficits without realising—and period loss becomes normalised, or even dismissed.

The good news? Recovery is possible, with the right support, the right lifestyle changes. With that, it isn’t just your period that returns—it’s your health.

Reference list

Baumeister, L. (2021). Have Period Symptoms But No Bleeding? Here’s Why. [online] Intimina. Available at: https://www.intimina.com/blog/have-period-symptoms-but-no-bleeding-heres-why/ [Accessed 14 Jul. 2025].

‌Cleveland Clinic. (2022). Hypothalamic Amenorrhea: Causes, Symptoms & Treatment. [online] Available at: https://my.clevelandclinic.org/health/diseases/24431-hypothalamic-amenorrhea [Accessed 14 Jul. 2025].

Karlsson, E. (2023). What is Hypothalamic Amenorrhea (HA) - The Science Behind. [online] HA Recovery Coach. Available at: https://www.ha-recovery.com/post/what-is-hypothalamic-amenorrhea-ha-the-science-behind [Accessed 14 Jul. 2025].