Do I have HA or PCOS?

Jul 7, 2023 | Blog

Getting down to the root cause of your missing period

As a period recovery dietitian, I have seen many women struggle with finding the proper diagnosis- in particular determining if they have Hypothalamic Amenorrhea (HA) or Polycystic Ovarian Syndrome (PCOS). Though they share similarities in their effects on menstrual cycles, it is essential to recognize the distinctions between these conditions, as HA is commonly misdiagnosed as PCOS. In this blog post, we will shed light on the differences between HA and PCOS, helping you understand whether HA might be the root cause of your missing period.

What is Hypothalamic Amenorrhea? 

Hypothalamic amenorrhea, or sometimes called Functional Hypothalamic Amenorrhea (FHA),  is a condition characterized by the absence of menstruation due to dysfunction in the hypothalamus, a part of the brain responsible for regulating hormone production. Key features of HA include:

  • Low energy availability: When the body lacks adequate energy availability, non-essential body systems are shut down. This includes things like hair growth, thyroid function, proper digestion, and reproduction. With HA, the low energy availability is caused by a combination of stress, excessive exercise, and inadequate caloric intake. Any of these triggers alone could cause menstrual irregularities, but with full blown amenorrhea, it’s typically some combination of all three. 
  • Low hormone levels: In HA, the hypothalamus reduces the secretion of gonadotropin-releasing hormone (GnRH), which subsequently decreases the levels of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) from the pituitary gland. Textbook HA will be easily seen by having labs drawn, but in many cases hormones can be low/normal and someone may still very much be experiencing HA. 
  • Absence of other PCOS symptoms: Unlike PCOS, individuals with HA typically do not exhibit symptoms such as excess hair growth (hirsutism), acne, or insulin resistance.  

Understanding Polycystic Ovary Syndrome (PCOS):

On the other hand, Polycystic Ovary Syndrome (PCOS) is an endocrine disorder that affects the ovaries. It is characterized by hormonal imbalances, insulin resistance, and the presence of multiple small cysts on the ovaries, varying in size between 2-9 mm in diameter.  PCOS can present with symptoms such as irregular periods, excessive hair growth, acne, weight gain, and chronic anovulation. The exact cause of PCOS is not fully understood, but it is believed to have a genetic component and can be influenced by lifestyle factors

Differentiating HA from PCOS:

HA is primarily caused by factors such as weight loss, excessive exercise, and chronic stress, while PCOS has a stronger genetic component. While HA is reversible through proper nutrition and lifestyle adjustments, PCOS is more of a chronic condition where symptoms can be managed and improved, but not completely reversed. 

The best way to distinguish the differences between HA and PCOS is by looking at a combination of labs, physical symptoms, and lifestyle factors. 


In HA, the hormonal profile often shows low levels of estrogen and progesterone due to disrupted feedback mechanisms. Depending on the severity of HA, LH and FSH can be low or normal. In contrast, PCOS is characterized by high levels of androgens (male hormones) and insulin resistance. While not technically part of the Rotterdam criteria,  a ratio of 2:1 or  3:1 LH to FSH can point towards PCOS. However, we do sometimes see LH overshoot during HA recovery, which is why looking at labs alone doesn’t always give a full picture of what may be going on with an individual. 

Physical Symptoms

HA is commonly associated with symptoms of energy deficiency, such as low energy levels,  loss of menstrual cycle, and potential bone density issues. Someone experiencing HA may have a lot of gut issues due to a combination of the physical stress from exercise, under eating, and lack of variety in their diet to support a healthy gut microbiome. Additional symptoms can include low body fat (even if BMI is normal), low thyroid hormones, poor hair growth, brittle nails, decreased libido, vaginal dryness, anxiety, and disordered eating habits. PCOS, on the other hand, may present symptoms such as unexplained weight gain, excessive hair growth, and cystic acne. 

Diagnostic Criteria

Diagnosing HA involves ruling out other causes of amenorrhea, such as pregnancy, thyroid disorders, PCOS, Primary Ovarian Insufficiency (POI), and other medical conditions. In addition to testing bloodwork your doctor may want to run an MRI to rule out a pituitary tumor. HA is a diagnosis of exclusion and unfortunately goes undiagnosed in many cases.

PCOS is diagnosed using the Rotterdam criteria, which requires 2 out of 3 of the following: the presence of missing or irregular periods, polycystic ovaries, and/or elevated male hormones. Of importance: many individuals with HA will meet this criteria, which is a big reason why HA can get misdiagnosed as PCOS. 

As a result, I see a lot of women end up thinking they are doing everything right for their PCOS, including exercising excessively, eating clean, and trying to lose weight, only driving themselves deeper into HA. HA recovery requires reducing exercise, eating more, and putting on necessary body fat to ovulate, have healthy cycles, and get pregnant.

Next steps if suspect you have HA

If you are experiencing a missing period and suspect that HA may be the cause, it is crucial to consult with a healthcare professional, preferably a registered dietitian and an endocrinologist, to evaluate your symptoms, medical history, and conduct the necessary tests. A dietitian can perform a thorough evaluation of your diet history, weight status, and current nutrient intake to determine gaps in your lifestyle that may be contributing to your missing period. An Ob Gyn or Reproductive Endocrinologist can do a  DXA bone density scan, order labs, and run an MRI to help rule out other causes of period loss so that you’re fully supported in getting down to the root cause of your missing period and fertility issues. 

In conclusion, understanding the differences between Hypothalamic Amenorrhea and PCOS is essential for an accurate diagnosis. While both conditions can affect menstrual cycles, their underlying causes, hormonal profiles, and associated symptoms differ significantly. If you suspect HA may be the root cause of your missing period, seek professional guidance to receive the appropriate diagnosis and find a registered dietitian who specializes in HA to help you fill in the gaps in your nutrition and lifestyle habits to support getting your period back for health and fertility! 

You Can Recover from HA and Restore Your Fertility

Apply to Join the Food Freedom Fertility Society.

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Disclaimer: This blog post is intended for informational purposes only and should not replace professional medical advice. Always consult with a qualified healthcare professional regarding your specific condition.

Saadia Z. Follicle Stimulating Hormone (LH: FSH) Ratio in Polycystic Ovary Syndrome (PCOS) – Obese vs. Non- Obese Women. Med Arch. 2020 Aug;74(4):289-293. doi: 10.5455/medarh.2020.74.289-293. PMID: 33041447; PMCID: PMC7520057.


Shufelt CL, Torbati T, Dutra E. Hypothalamic Amenorrhea and the Long-Term Health Consequences. Semin Reprod Med. 2017 May;35(3):256-262. doi: 10.1055/s-0037-1603581. Epub 2017 Jun 28. PMID: 28658709; PMCID: PMC6374026.


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I’m a fertility nutritionist and registered dietitian who specializes in hypothalamic amenorrhea. My passion is helping women trying to conceive find freedom with food and exercise, so they can recover their period, and get pregnant naturally.

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