What Labs to Request if You Suspect Functional Hypothalamic Amenorrhea (HA)

Jul 16

Why Understanding Your Labs Matter

Have you recently gone to the doctor because of a missing period, only to leave with a vague diagnosis or worse, one that doesn’t actually make sense?

This is What Happened To Our Clients

Client N was misdiagnosed with PCOS for over 15 years. She was told to cut carbs and exercise more, which drove her deeper in HA (Hypothalamic Amenorrhea). Another client was told she had premature ovarian failure (POI) based on an FSH of 2 mIU, a value that's actually very common in hypothalamic amenorrhea. Both were left believing their missing period was permanent and something they couldn’t change.

That’s why we created our FREE Lab Guide: so you can compare your labs, get clarity, and take the right next steps.

The key labs to ask for (and why they matter)

FSH (Follicle Stimulating Hormone): This hormone drives the growth and maturation of follicles in your ovaries. In HA, FSH typically runs low because the HPO axis (hypothalamic pituitary ovarian axis) is suppressed by low energy availability. When your brain senses there isn’t enough fuel to support every system, it down-regulates FSH to conserve resources and prioritize survival over reproduction. This low hormonal signaling is a core reason behind a missing period in hypothalamic amenorrhea.

LH (Luteinizing Hormone): LH is the hormone that triggers ovulation. In HA, LH is often low or low normal because, like FSH, it’s regulated by the HPO axis, which becomes suppressed by low energy availability. When the brain perceives a lack of resources, it down-regulates LH to prevent ovulation, conserving energy for essential functions. Low LH is one of the clearest hormonal indicators of a suppressed reproductive system.

Estrogen (specifically Estradiol or E2): Estrogen is primarily produced by developing follicles. Without FSH and LH to signal the ovaries, estrogen levels remain low, and the uterine lining doesn’t build, hence, no period. Low estrogen over time also affects bone health, mood, and metabolism.

Prolactin: This hormone plays a key role in lactation but can also disrupt the reproductive cycle when levels are too high. Elevated prolactin, a condition known as hyperprolactinemia, can mimic HA symptoms or point to a more serious issue like a pituitary tumor. However, prolactin can also rise in response to chronic stress, even without a tumor or underlying medical condition.

Understanding the link between stress and prolactin can help you and your provider rule out unnecessary concerns and focus on root causes. 👉 [Read up more on prolactin and chronic stress]

Because elevated prolactin can halt ovulation and menstrual cycles, it’s important to rule this out early in the diagnostic process.

HA is a diagnosis of exclusion

Hypothalamic amenorrhea is caused by low energy availability due to stress, undereating, overexercising or a combination of all 3, but it’s also a diagnosis that requires ruling out other conditions like PCOS, premature ovarian insufficiency (POI), or hyperprolactinemia. Your doctor may not automatically run these labs, which is why it’s so helpful to know exactly what to request and what to look for in your results. That’s where our FREE Lab Guide comes in. Inside, we outline the ideal ranges to help you spot patterns, not just numbers.

“But my doctor said my labs are normal…”

This is something we hear all the time, and if that’s been your experience, here are two key things you need to know:

1. Lab reference ranges are wide:

For example, estrogen in the follicular phase can range from 20 to 80 pg/mL, and just before ovulation it can spike anywhere from 200 to 500 pg/mL. That’s a huge range, and being technically “within normal limits” doesn’t mean your hormones are optimal, especially if you’re dealing with a missing period and suspect HA.

2. Labs are interpreted assuming you’re cycling:

Most doctors evaluate labs based on what they’d expect to see at different phases of a healthy cycle. So if your estrogen is on the low end, they may say it’s “fine,” assuming you’re in the early follicular phase. But if you’re not cycling at all, low estrogen is a red flag, not a normal variation.

This is why it’s so important to work with someone who can look at your labs through the lens of HA. If you want a second opinion on your labs you can book a one-time consultation here.

HA vs. PCOS: What’s the difference?

If you're dealing with a missing period, it's important to distinguish between HA and PCOS, as their root causes and treatments are very different.

It’s common for people with HA to be misdiagnosed with PCOS or to be scared into thinking they have it because of an ultrasound or symptoms like acne. But the root causes of the two conditions are very different.

In HA, the brain suppresses the HPO axis (hypothalamic pituitary ovarian axis) in response to perceived stress or low energy availability. This suppression leads to low or normal levels of FSH, LH, and estrogen, resulting in a lack of ovulation. In contrast, in PCOS, the HPO axis is dysregulated in the opposite direction: a persistently high GnRH pulse leads to excessive release of LH and a relative deficiency of FSH. This imbalance increases androgen production, often resulting in symptoms like hirsutism, hair loss, and acne.

As you can see, the underlying mechanisms of HA and PCOS are very different. In HA, the system is suppressed; in PCOS, it’s in overdrive, particularly in how GnRH, LH, and FSH are regulated. Additionally, someone with PCOS will still have a period, though it may be irregular, while in HA, there is no period at all.

There’s also emerging research showing that women recovering from HA can temporarily show signs of PCOS, like high LH or AMH, but that doesn’t mean you’ve developed PCOS overnight. It means your body is recalibrating. The priority is always to treat HA first, then reevaluate later if needed (1).

What’s Next

If you’ve been left wondering why you have a missing period, and your labs haven’t given you answers, our lab guide can help you decode what's going on.

As you can see there’s a lot of nuance, and when it comes to hypothalamic amenorrhea (HA), that nuance matters. Many doctors interpret labs through the lens of someone who’s cycling, which can leave you misdiagnosed or confused. That’s why we created our FREE Lab Guide, so you can review the exact labs and ideal values for HA, PCOS, and POI side by side.

Download the guide here to take the guesswork out of your labs.

Want an expert HA eye on your labs? [Book a one-time consult here].

Ready to stop spinning in circles and actually resolve HA? [Explore our coaching options here].

At The HA Society, we provide education, community, and individualized support to help women move through the complexities of recovery, from stress-driven hormone disruptions to body image and behavior change. Whether you’re in the thick of healing or supporting others through it, we’re here to walk with you.