Could Your PCOS Actually be Hypothalamic Amenorrhea?

The menstrual cycle is a vital sign for the reproductive health of a female. Both Hypothalamic Amenorrhea (HA) and Polycystic Ovary Syndrome (PCOS) are signs of reproductive dysfunction with some overlap in symptoms, yet with significantly different underlying drivers. It’s very easy to incorrectly mistake a case of HA for PCOS, however it’s crucial that the conditions are correctly diagnosed to determine the correct treatment strategy. 

Hypothalamic Amenorrhea

A reversable and very common form of amenorrhea (lack of period for 3 or more consecutive months) in premenstrual females. According to the American Society of Reproductive Medicine, HA is responsible for 20–35% of secondary amenorrhea and an estimated 17.4 million women worldwide between the ages of 18 and 44 are affected.  

In simple terms, HA presents when the level of psychological stress, excessive exercise and/or disordered eating is enough for the hypothalamus (the hormonal control centre of the body) to determine that it’s not a safe time to reproduce. 

The stress causes a suppression of gonadotropin releasing hormone (GnRH) in the hypothalamic-pituitary-ovarian (HPO) axis which sets off a chain reaction of low follicle stimulating hormone (FSH) and luteinizing hormone (LH) being released from the anterior pituitary and subsequently low levels of oestradiol production. As a result, endometrial thickening does not occur during the first half of the cycle (follicular phase) resulting in amenorrhea. 

A diagnosis of HA is defined as: 

  • Absent periods for at least 3 consecutive months (amenorrhea)
  • Low oestradiol (E2) 
  • Low FSH 
  • Low LH
  • With the exclusion of all other possible causes including thyroid dysfunction, hyperprolactinemia, premature ovarian insufficiency (POI), and PCOS.

In treating HA there is a common tendency in the medical world to prescribe the Oral Contraceptive Pill (OCP) as a means for correcting estrogen deficiency. It’s important to recognise that while this may help to regain a regular menstrual cycle, it won’t address the underlying cause for amenorrhea nor prevent bone loss from occurring.  Treatment requires the root cause for the HPO dysfunction to be addressed which may mean a combination of stress management, reappropriation of energy intake and nutrient density and/or reduction in exercise.  

Polycystic Ovary Syndrome

Prevalence of the condition ranges between 6 and 15% of women worldwide, making it one of the most common hormone conditions in women of reproductive age.  It’s a stressful condition, highly associated with depression, anxiety & poor self-esteem and can significantly increase risk of infertility. 

The most widely accepted definition of PCOS is the Rotterdam definition of 2003:

Diagnosis of PCOS can be made when two of the following three exist: 

  • Infrequent menstrual cycles of 35+ in length or having 8 or fewer periods per year
  • Clinical or physical evidence of androgen excess such as elevated free testosterone, male-patterned hair growth, acne or alopecia
  • Polycystic ovaries on ultrasound examination. 

Other aetiologies must be excluded such as congenital adrenal hyperplasia, androgen secreting tumours, Cushing syndrome, thyroid dysfunction and hyperprolactinaemia.

The Androgen Excess and PCOS Society has proposed a further definition which concentrates on androgen excess. The causes for androgen excess are varied and lead to what can be classified as 4 key types of PCOS: 

  1. Insulin-resistant PCOS: High circulating levels of the hormone insulin will drive androgen production. Testing fasting insulin and HbA1c as well as fasting blood glucose will help to determine if this is the cause of PCOS, which it is in vast majority of cases. Treating this form of PCOS requires the reversal of insulin resistance which can happen with weight loss, LCHF and the support of certain supplements.
  2. Post-pill PCOS: Coming off certain forms of the OCP can drive a temporary surge in androgens leading to symptoms of androgen excess. It’s very common for women to experience irregular cycles when coming off the pill and the importing thing to recognise here is that if periods were normal before starting the pill then the androgen surge is temporary and will likely resolve in time. 
  3. Inflammatory PCOS: Chronic inflammation can stimulate the ovaries to make too much testosterone.  The presence of unexplained fatigued, headache, IBS or SIBO, joint pain and/or chronic skin conditions in the absence of high insulin or recent OCP use could all be signs that the PCOS is driven by chronic inflammation. Treatment in this case relies on understanding the root cause and treating that. 
  4. Adrenal PCOS: If testosterone levels are normal but DHEAS is elevated and the above criteria are not met, then it’s a sign of adrenal PCOS. Stress reduction and nervous system support are required to help resolve these cases of PCOS. 

Although HA and PCOS can exist alongside one another, it’s incredibly common for HA to go undiagnosed or to be misdiagnosed. Similarly, it is common for women to be diagnosed with PCOS yet not then understand the driver for their PCOS. 

Like we always say at The Natural Nutritionist, your menstrual cycle is your monthly report card. It’s a huge barometer of health and when it’s missing entirely or irregular, regaining regularity is key. It’s not just about fertility in the long term, but it’s crucial to bone health, cardiovascular disease risk and psychological wellbeing. 

The Keys to Understanding 

Though symptoms are similar, treating HA like a case of PCOS could be disastrous to achieving resolution and likely lead to none at all. If you’re resonating with the above, then please know it’s crucial to understand the driver for your irregular or absent periods so treatment can be applied appropriately. For a basic level of understanding, the key measures to assess via simple blood test are: 

  • Fasting insulin
  • Free testosterone  
  • DHEAS 
  • LH: FSH ratio (done on days 2 – 3 of the cycle if a cycle is present)
  • Morning cortisol. 

In addition, salivary hormone profiling can be done as a more sensitive means for measuring oestradiol, testosterone, DHEAS and cortisol. 

If you’d like assistance in addressing your menstrual cycle regularity, then please book in for a complimentary 15 minute consultation to discuss your testing requirements and next steps. You might also like to listen to the episode of 298 of Health, Happiness & Human Kind dedicated to this topic.


Shufelt CL et al. 2017. Hypothalamic Amenorrhea and the Long-Term Health Consequences. Semin Reprod Med. 35,3, 256-262.

Rotterdam ESHRE/ASRM-Sponsored PCOS Consensus Workshop Group. 2004. Revised 2003 consensus on diagnostic criteria and long-term health risks related to polycystic ovary syndrome. Fertility and Sterility. 81, 1, 19-25.

Alemyar A et al. 2020. Anti-Müllerian Hormone and Ovarian Morphology in Women With Hypothalamic Hypogonadism. Journal of Clinical Endocrinology and Metabolism. 1, 105, 5.

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