What Actually Happens in the Body When the Menstrual Cycle Stops?

By Project REDs Ambassador and Guest Writer, Meg Smith (PhD Researcher at Loughborough University and Female Athlete Health, Consultant for AG Insurance–Soudal Women’s WorldTour Cycling Team) In conversations around female athlete health, one topic comes up time and time again: the menstrual cycle disappearing. For some athletes, this happens gradually. Their cycle becomes irregular, then infrequent, and eventually stops altogether. For others, it can feel more sudden, often coinciding with periods of increased training load, life stress, or changes in nutrition. The menstrual cycle (or its disruption) does not look the same for every female athlete.

Where things become challenging, is how this change is interpreted. Menstrual disruption is sometimes normalised, brushed off, or in some environments even quietly reinforced as a sign of hard work or commitment to training. It’s easy to overlook in the moment, especially in the context of heavy training schedules, competition, and the constant push to improve performance.

But when the menstrual cycle stops, it’s not random, and it’s not without consequence. It reflects a shift in how the body is functioning beneath the surface".

The brain comes first: how the system is downregulated

The menstrual cycle is regulated by a communication pathway known as the hypothalamic- pituitary-ovarian (HPO) axis. At the top of this system sits the hypothalamus, a region of the brain that continually monitors the body’s internal environment, including energy availability, stress levels, and overall physiological strain.

When the hypothalamus detects that the body is underfuelled or under significant stress, it reduces its release of gonadotropinreleasing hormone (GnRH). GnRH is the signal that normally tells the pituitary gland to release luteinising hormone (LH) and folliclestimulating hormone (FSH), which in turn stimulate the ovaries. When this signal is suppressed: - Ovulation may be delayed or stop entirely - Oestrogen and progesterone production decrease - The menstrual cycle becomes irregular or disappears This process is known as functional hypothalamic amenorrhoea (FHA). Importantly, this is not a failure of the reproductive system. It is a protective, adaptive response from the brain when it perceives that the body does not have sufficient energy to support all the physiological demands its under. As the reproductive system is very energy demanding and non-essential for a female’s survival, it is one of the first systems to downregulate.

Energy availability: the central driver

At the heart of this process is energy availability (i.e., the energy left over from food intake after the cost of training has been met, which is required to support basic physiological function). When energy availability is chronically low (whether due to high training loads, insufficient fuelling, psychological stress, or a combination of all three), the body is forced to prioritise essential survival processes over reproduction. Reproduction is energetically costly. From an evolutionary and survival perspective, it is one of the first systems to be downregulated when energy is limited. But the reproductive system is not the only one affected.

What Else Is Affected When the Cycle Stops?

The same signals that suppress the menstrual cycle also alter the function of several other physiological systems: Bone health: Oestrogen plays a critical role in maintaining bone mineral density. When oestrogen levels are low, bone breakdown increases and bone formation slows down, significantly raising the risk of stress fractures and longerterm losses in bone mineral density. Metabolic and endocrine function: The body becomes more energyefficient. Resting metabolic rate may decrease, and disruptions can occur in thyroid hormones, which regulate energy use and temperature control. Cardiovascular health: Oestrogen also has protective effects on the cardiovascular system. Chronically low levels have been shown to negatively impact vascular function over time.

Immune function: Low energy availability is linked with increased illness frequency and slower recovery from infection.

Psychological and cognitive function: Athletes may experience persistent fatigue, low mood, irritability, and reduced concentration. These symptoms are often dismissed as ‘normal training fatigue,’ but can reflect underlying hormonal disruption.

Performance: the hidden cost

In the short term, an athlete may continue to perform well despite a disrupted or absent cycle. This is often where misconceptions arise because performance does not seem to be compromised… yet. Over time, the physiological cost accumulates. Compromised recovery, increased injury risk, more frequent illness, and reduced training consistency all limit longterm progression and performance. The very adaptations the body makes to cope with low energy availability ultimately undermine performance.

In simple terms: you cannot sustainably perform at your best when the systems that support adaptation, recovery, and resilience are compromised."

It’s not always obvious

One of the challenges with menstrual dysfunction is that it does not always present as a complete absence of periods. Some athletes may experience: - Irregular cycle lengths - Subtle hormonal disturbances despite bleeding - Anovulatory cycles (where ovulation does not occur) This is why simply ‘having a bleed’ does not always mean the system is functioning optimally. Consistent tracking, alongside informed interpretation, is key to identifying these patterns early.

The bottom line

When the menstrual cycle disappears, it is not random. It reflects a coordinated protective response driven by the brain in reaction to low energy availability and accumulated stress. While protective in the short term, this response can carry significant longterm consequences if left unaddressed. The menstrual cycle is one of the most sensitive indicators of whether the body has sufficient energy to support both health and performance. When it becomes disrupted, it is a signal that the body is under pressure, and something needs to change. For athletes and coaches, the goal is not simply to restore the cycle, but to create an environment where the body has the resources it needs to adapt, recover, and thrive.

Because ultimately, a healthy athlete is a high performing athlete and nothing beats sustainable performance.

Reference: Saadedine, M., Kapoor, E., & Shufelt, C. (2023). Functional Hypothalamic Amenorrhea: Recognition and Management of a Challenging Diagnosis. Mayo Clinic proceedings, 98(9),