Hypothalamic amenorrhea vs PCOS: what’s the difference?

Irregular cycles or missing periods can be a key symptom for people with PCOS. However, a lack of menstrual bleeds or periods isn’t unique to PCOS and could be hypothalamic amenorrhea. If you’ve heard both of these terms as a potential diagnosis for yourself or are still unsure, let’s find out more together about hypothalamic amenorrhea vs PCOS.

What is PCOS?

PCOS or Polycystic Ovarian Syndrome or Polycystic Ovary Syndrome is a complex endocrine or hormone condition impacting 1 in 10 people with ovaries. Despite its name, it does not solely involve the ovaries. Common symptoms individuals with PCOS experience include but are not limited to irregular periods, infertility, acne, excess facial hair and body hair plus unintentional weight gain.

It is thought to be linked with chronic inflammation and insulin resistance. It is important to mention that not every person experiences the same symptoms. This can make it challenging to diagnose.

How is PCOS diagnosed?

The diagnostic criteria for PCOS were established decades ago, around 1935, but in 2003 PCOS experts met in Rotterdam producing a joint consensus, now commonly known as the ‘Rotterdam Criteria’ to diagnose PCOS which is widely accepted around the world for the diagnosis of PCOS.

2023 article summarises the current guidelines. The Rotterdam Criteria broadened the phenotypic expression of PCOS to include any 2 out of the 3 key features of PCOS:

  1. Oligo-amenorrhea, also known as irregular infrequent periods or menstrual bleeds.
  • Absence of periods (amenorrhoea)
  • Irregular periods (fewer than 6-8 periods per year)
  • Regular periods with suspected PCOS can lead to blood tests to look at your hormone levels 
  1. Hyperandrogenism diagnosed in adults with hirsutism, alopecia, and acne using biochemical and physical markers 
  • This is higher levels of ‘male sex hormones’ such as testosterone and in a blood test, total testosterone levels are often high
  1. Polycystic appearance on the ovaries on an ultrasound

Polycystic ovarian morphology (PCOM) is defined as the presence of one ovary with an ovarian volume larger than 10mL or having more than 12 follicles (measuring 2-9mm in diameter) that satisfy the criteria.

To be diagnosed with PCOS it is essential to work with a healthcare provider to determine the cause of your symptoms.

What causes PCOS?

The likelihood of developing PCOS is likely to be affected by a blend of genetic factors and environmental elements. Although the precise cause remains unknown, there seems to be a familial tendency, if a family member, such as your mother, sister, or aunt, has PCOS, your chances of developing the condition are increased.

What is hypothalamic amenorrhea?

Hypothalamic amenorrhea (HA) is when your hypothalamus causes your periods (menstrual bleeds) to stop. 

Your hypothalamus is located in your brain that acts as your body’s control coordination centre. Its primary function is to keep your body in a stable state, known as homeostasis. It does this through direct influence on your autonomic nervous system and managing hormones. 

With HA, your hypothalamus releases gonadotropin-releasing hormone (GnRH), which works with follicle-stimulating hormone (FSH), luteinizing hormone (LH) (FSH and LH are secreted by the pituitary gland) and oestrogen to control menstruation. This mechanism is referred to as the hypothalamic-pituitary-ovarian (HPO) axis which is essential for reproductive health. 

In hypothalamic amenorrhoea, the hormonal imbalance comes when your hypothalamus stops producing GnRH. subsequently leading to irregular or absent periods.

Hypothalamic amenorrhea

How is hypothalamic amenorrhea diagnosed?

Hypothalamic amenorrhea is diagnosed usually by ruling out other conditions that could be interrupting the menstrual cycle. Commonly HA is associated with a person who has restricted their nutrition, does excessive exercise and their body is in a constant state of stress. 

There are 2 main types of amenorrhea:

  • Primary amenorrhea is when you haven’t had your first period by 16 years old or within 5 years of puberty 
  • Secondary amenorrhea is when you’ve had regular periods, but then this stops being regular for more than 3 months. Hypothalamic amenorrhea is a type of secondary amenorrhea and accounts for approximately 30% of cases according to recent 2020 evidence

The following blood hormone tests done to diagnose include:

Gonadotropin-releasing hormone (GnRH)To measure the function of the hypothalamusLow levels may indicate a dysfunctional hypothalamus 
Follicle-stimulating hormone (FSH)Low levels may indicate HA 
Luteinizing hormone (LH)
Thyroid-stimulating hormone (TSH)To check for thyroid gland disorders 
ProlactinTo check your pituitary gland 
TestosteroneTo check for hyperandrogenism which could indicate PCOS 
Human chorionic gonadotropin (hCG)To check for the possibility of pregnancy 
Blood tests required to diagnosis HA

What causes hypothalamic amenorrhea?

HA is a multifactorial disorder and often a combination of factors may be contributing to the onset of the condition.

A common cause of HA is low body weight which may be caused by restrictive eating and strenuous exercise of varying levels. Significant weight loss or being underweight can disrupt the normal functioning of the hypothalamus. This is often seen in individuals with eating disorders, such as anorexia nervosa, or in athletes who engage in intense training without adequate caloric intake.

Stress is also a key inhibitor of reproductive function. Whether emotional or physical, stress can disrupt the normal hormonal signals responsible for regulating the menstrual cycle. Stress as an underlying cause of HA may be contributing to period problems – so make sure you’re looking after yourself where you can.

Hypothalamic amenorrhea vs PCOS: key differences and similarities

Both hypothalamic amenorrhoea (HA) and PCOS can be considered diagnoses of exclusion, meaning your doctor will be ruling out other potential causes of your symptoms. Often I advise my clients to keep track of their menstrual cycle to be aware of any changes that could occur. The more knowledge and awareness around our menstrual cycle, the better we can advocate for ourselves if we notice any concerns.

Whilst both conditions have distinct pathophysiology and diagnosis supported by guidelines, in practice differentiating these 2 conditions causing menstrual disturbances is challenging because they both contribute to hormonal imbalances. 

It can be an irregular, absent or regular cycle. Every person is unique No menstrual period for more than 3 months  
Raised AMH (anti-Mullerian hormone), although mild in HA Long-term HA impacts the bone mass density, which if left untreated can result in osteoporosis and increase the risk of fractures
Insulin resistance  and igh fasting insulin Low fasting insulin
Low energy levels or fatigue Low energy levels or fatigue 
Excessive hair growth or hair lossHair loss 
Depression and anxiety Stress levels could be a contributing factor
Can occur in individuals of all body shapes and sizes  Can be recent weight loss
It is a diagnosis of exclusion It is a diagnosis of exclusion 
Higher endometrial thickness Lower endometrial thickness 
A table with the key differences and similarities between PCOS and HA

Can you have HA and PCOS?

Hypothalamic amenorrhoea can overlap with polycystic ovarian morphology (PCOM) as frequently as 50% of cases according to a 2021 study. This study suggests that HA is uncommonly found in individuals with BMI over 24, whereas PCOS and HA can occur with lower body weights and BMI. So yes it is possible, however, HA is reversible and PCOS is a chronic endocrine disorder.

PCOS-D type which is PCOS without hyperandrogenism in comparison to individuals with hypothalamic amenorrhea with polycystic ovaries or PCOM can be the most difficult to distinguish. It was found in a 2021 study that PCOM is more frequently found in individuals with hypothalamic amenorrhea than in individuals without. 

Treatment of hypothalamic amenorrhea vs PCOS

If you have been provided with a formal diagnosis of either of these distinct conditions, your doctor or consultant will discuss the potential treatment options available to you.

No.Hypothalamic AmenorrheaPolycystic Ovarian Syndrome 
1.Hormonal contraception, for example, the combined contraceptive pill
2.Lifestyle modifications related to diet, exercise and stress. It is often the case that hypothalamic amenorrhea can be caused by to lack of energy, excessive exercise and high stress levels. Being mindful of these factors is also important for PCOS.
3.Gaining weightMetformin
4.Hormone replacement therapyAnti-androgen medication
A table with the key treatment options for PCOS and HA

Key takeaways: hypothalamic amenorrhea VS PCOS

Both hypothalamic amenorrhoea and PCOS can cause irregular menstrual bleeds or periods. Although they are two different conditions, it is plausible to have both of these. There can be a stereotype for each of these conditions but actually, they can impact individuals of all different body shapes and sizes. 

It’s important to keep in mind that you may not present all the symptoms of either condition and that makes diagnosis and treatment difficult to obtain. Remember more awareness and tracking of your menstrual cycle and symptoms is useful to seek the appropriate care for you. 

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Sophia Boothby RD Author at The PCOS Collective

Lead Author | Head Dietitian | Registered Dietitian


Sophia is a Registered Dietitian working as a Specialist Community Dietitian within a London NHS Teaching Hospital specialising in gut health such as irritable bowel syndrome (IBS) and the low FODMAP diet, type 2 diabetes, PCOS, and cardiac rehabilitation. Sophia offers 1:1 PCOS support in our virtual PCOS clinic.

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