Is it PCOS . . . or Hypothalamic Amenorrhea? Here’s Why It’s So Common to Confuse the Two.

Missing periods? Dealing with hormonal chaos? You've likely heard the term PCOS (polycystic ovarian syndrome) tossed around as the catch-all for irregular cycles. But what if your symptoms actually point to Hypothalamic Amenorrhea (HA) - a condition that’s often misdiagnosed as PCOS, leading to the wrong treatment, unnecessary stress, and frustrating dead ends?

If that sounds familiar, you’re not alone.

Let’s unpack what HA actually is, how it overlaps with PCOS, and why getting clarity matters for your healing journey.

What is Hypothalamic Amenorrhea (HA)?

HA happens when your brain - specifically your hypothalamus - tells your body to press pause on menstruation. This usually happens because it perceives chronic stress, under-fueling, or overexercising as a threat to your safety.

When this occurs:

  • Ovulation stops

  • Estrogen levels drop

  • Periods disappear (amenorrhea)

HA is not a reproductive system failure—it’s your body trying to protect you. It’s often seen in:

  • People under chronic stress

  • Athletes or people doing intense exercise (especially without enough recovery or nutrition)

  • Those who are unintentionally under-eating or dieting

  • Folks with a history of disordered eating or restriction (even if they don’t identify with that label)

How is HA Different from PCOS?

Both conditions can involve missing or irregular periods, but the underlying causes and treatments are very different.


Important Note: People with HA can have ovaries that look “polycystic” on ultrasound - which is why HA is frequently misdiagnosed as PCOS. But the presence of cysts isn’t enough for a diagnosis!

Why the Misdiagnosis Matters

Getting the diagnosis right matters because treatment plans are totally different.

  • PCOS care often includes blood sugar regulation, managing androgens, and ovulation support.

  • HA care is rooted in nourishment, stress reduction, and recovery - not restriction or intense exercise.

If you’re told to “cut carbs,” “exercise more,” or “take hormonal birth control” for what’s actually HA, your recovery could be delayed - or made worse.

How I Support HA in Practice

In my virtual naturopathic care, we take a gentle, systems-based approach to uncover what’s going on behind the missing period. For HA, we explore:

  • Your nutrition and eating patterns (without judgment)

  • Exercise routines and recovery time

  • Stressors (including emotional and nervous system stress)

  • Hormone testing and blood work (to assess LH, FSH, estradiol, TSH, prolactin, etc.)

  • Your unique story and what feels safe to your body

Then we build a care plan around safety, nourishment, and support - not shame or restriction.

Still Not Sure Which One You’re Dealing With?

If you’ve been diagnosed with PCOS, but the treatments haven’t helped - or your period disappeared after a stressful time in life or changes in eating/movement — it’s worth considering HA.

You can book a free intro call with me anytime to talk it through. Your period isn’t broken. It might just need a different kind of support.


Jennah Miller