Does Exercise Protect Bone Health in Hypothalamic Amenorrhea?

We constantly hear messages about how we need to be exercising enough for health and wellness. But most of this advice is geared toward the general public—not those navigating hypothalamic amenorrhea (HA). When you’re working to restore your period, the very habits that are praised in mainstream health culture can actually stand in the way of recovery. It’s frustrating, confusing, and can feel isolating. If you’ve lost your period, you might wonder if continuing to exercise will protect your bones. While exercise is generally good for bone health, the benefits are not the same when HA is involved. In fact, continuing to exercise without addressing the root cause of HA can accelerate bone loss rather than prevent it. Let’s explore why.

What is Hypothalamic Amenorrhea?

Hypothalamic amenorrhea (HA) happens when your period stops for at least three consecutive months due to stress on the body, often caused by not eating enough, exercising too much, or experiencing high levels of psychological stress. Your brain (specifically the hypothalamus) senses that your body doesn’t have enough energy to support reproductive functions, so it reduces the production of hormones necessary for ovulation and menstruation. This can lead to low estrogen levels, which not only affects fertility but also compromises bone density over time. 

How is HA Diagnosed?

Since HA is a diagnosis of exclusion, doctors first rule out other potential causes of missing periods, such as PCOS, thyroid disorders, or pregnancy. This process typically includes a medical history review, hormonal blood tests, bone density scans (DEXA), and lab work to eliminate other conditions. If no other explanation is found and signs of low energy availability are present, HA is the most likely cause.

Why Exercise Won’t Prevent Bone Loss in HA

Estrogen is Essential for Bone Strength

In the case of HA, estrogen is often too low for a menstrual cycle. Estrogen plays a critical role in bone remodeling and density. When estrogen levels drop due to HA, bones lose more density than they rebuild, making them weaker over time. This means that even if you’re lifting weights or engaging in impact-based activities, your bones can’t effectively strengthen without adequate estrogen.

Insufficient Energy Availability Impairs Bone Formation

HA is caused by insufficient energy availability meaning your body isn’t getting enough fuel to support all its functions. In response, the body prioritizes essential systems (like keeping your heart beating) over bone repair and growth. If you’re not fueling enough to match your activity level, exercise can actually contribute to further bone loss.

Higher Risk of Stress Fractures and Osteoporosis

Studies show that individuals with HA—especially athletes and those engaging in high-intensity exercise—are at a higher risk for stress fractures, osteopenia, and osteoporosis. Since the body is in a state of insufficient energy availability, it pulls nutrients from bone stores, further weakening them over time. The longer HA persists, the greater the risk of developing irreversible bone loss.

It Can Reduce Sex Hormone Formation

Exercise, especially high-intensity or prolonged workouts, triggers the release of cortisol, a stress hormone. Research supports that women with HA experience higher cortisol levels than women without HA. Cortisol suppresses sex hormone production (like estrogen and progesterone), further delaying the return of your menstrual cycle. This means that continuing to engage in high intensity or prolonged exercise can prolong the amount of time it takes to recover from HA. In addition, prolonged high cortisol can also contribute to bone loss, compounding the negative effects of low estrogen. 

Common Misconceptions About HA

"If I'm not underweight, I can't have HA"

HA can occur in individuals of all body sizes and even at a weight higher than your set point weight range. This is because HA is caused by insufficient energy availability, not just low weight.

“I don’t exercise much, so I can't have HA”

HA can occur regardless of exercise, including the amount or type of exercise performed. This is because HA is caused by insufficient energy availability, not just exercise intensity or duration.

"I still get a withdrawal bleed on the pill, so I don’t have HA."

Some people are prescribed birth control as a way to ‘fix’ HA or protect bone health. While research suggests that the pill may improve bone density in certain cases, there is also evidence to the contrary, making the overall findings inconclusive. Because HA is associated with an array of additional long term health concerns, given these mixed findings, I recommend healing from HA naturally by correcting energy imbalance.

"Exercise strengthens bones, so I should keep working out."

As discussed in the blog, without adequate estrogen and nutrition, exercise may contribute to bone loss rather than strengthen bones. By restoring your menstrual cycle, you can increase your bone density naturally.

"I don’t have an eating disorder, so I don’t have HA.”

You don’t need to have an eating disorder to develop HA. It is possible for disordered eating, chronically dieting, or unintentionally under-fueling your body to cause energy imbalance.

"I can’t exercise at all with HA, or again in the future”

Dr. Nicola Rinaldi’s research suggests that low-intensity, short-duration activities like walking and yoga do not delay HA recovery. In contrast, high-intensity, long-duration exercise can delay the recovery process. When reintroducing more intense exercise, Rinaldi advises waiting until a person has had at least three consecutive menstrual cycles (Rinaldi, 2016). At that point, gradually increasing activity while maintaining adequate nutrition and energy balance is the best approach to support a sustained menstrual cycle.

"My labs are normal, so I don’t have HA”

Hormone levels can sometimes appear within normal ranges, but the absence of a period is still a key sign of HA.

"You cannot have both HA and PCOS, or another condition that affects the menstrual cycle, at the same time."

PCOS and other conditions can cause irregular periods or loss of menstrual cycle however high levels of stress and insufficient energy availability can also be a cause. In this case I recommend addressing HA first to restore hormone balance so the genetic condition can be managed sustainably with gentle nutrition.

"My period isn’t missing, so i’m fueling adequately”

Under-eating and overexercising can lead to hypothalamic amenorrhea (HA) for many, but some individuals may still have their period due to various factors. For example, individual differences in energy sensitivity and genetics influencing hormonal regulation. However, even if the period remains, this doesn’t mean the body is functioning optimally, as other health issues like bone loss and metabolic changes can still occur. And remember, your mental health matters just as much as your physical health. If you're noticing other signs of low energy availability or if your relationship with food and exercise is taking a toll on your well-being, take it as a gentle signal from your body—it needs more nourishment and rest.

HA Recovery is About More Than Just Restoring Your Cycle

If you are struggling with HA, you are not alone. The best way to protect your bone density is to focus on adequate rest and nourishment. HA recovery is a process of healing and self discovery as you are able to learn more about your body’s unique needs and rebuild trust with yourself. Be patient and kind to yourself along the way, remembering that you are creating a healthier, more sustainable relationship with food, movement, and self-care. You deserve to feel fully nourished, energized, and at peace. 

Looking for Additional Resources?

To learn more about HA, I recommend the book No Period. Now What? by Dr. Nicola Rinaldi, a researcher and expert on hypothalamic amenorrhea who has helped thousands of people recover their cycles through evidence-based nutrition, exercise, and mindset shifts.

Rinaldi, N. (2016). No period. Now what? A guide to regaining your cycles and improving your health. NPNW Publishing.

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