Polycystic ovary syndrome (PCOS) and hypothalamic amenorrhea often have overlapping symptoms, with a hallmark of missing or irregular periods. Given this, it can be challenging and confusing to figure out which of the two is going on. After all, they are two distinct conditions affecting women’s reproductive health, each with unique causes, symptoms, and treatment strategies. Both conditions can be influenced by stress, and understanding these differences is essential for effective management. To understand your own hormones clearly and to resolve your symptoms, an accurate diagnosis is key.
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Defining PCOS and Hypothalamic Amenorrhea
PCOS is a hormonal disorder characterized by irregular menstrual cycles, excess androgen levels, and polycystic ovaries. It affects up to 13% of women of reproductive age and can lead to symptoms such as weight gain, acne, and excessive hair growth (hirsutism). In contrast, hypothalamic amenorrhea is the absence of menstruation caused by a disruption in the hypothalamus, often linked to factors such as stress, significant weight loss, or excessive exercise. Women with hypothalamic amenorrhea typically experience a lack of menstrual cycles without the elevated androgen levels seen in PCOS. That being said, a woman can experience one or both conditions at different points in her lifetime.

The Role of Stress
Stress is a common factor influencing both PCOS and hypothalamic amenorrhea. In PCOS, stress exacerbates insulin resistance and subsequent testosterone levels, leading to worsened symptoms. There also is an entire subtype of PCOS, called adrenal PCOS, characterized by an excess adrenal (or stress) response in the body. For those with hypothalamic amenorrhea, chronic stress serves as a major disruptor of the hypothalamic-pituitary-ovarian axis, inhibiting the release of the brain hormones (LH and FSH) necessary for ovulation and menstruation. Managing stress through lifestyle changes is crucial for both conditions.
To learn more about the different subtypes of PCOS, read: The Root Cause of PCOS
Diagnostic Workup
The diagnostic process for PCOS typically involves a combination of medical history assessment, physical examination, and laboratory tests. Doctors often look for signs of hyperandrogenism (elevated testosterone and/or DHEA), irregular menstrual cycles, and perform ultrasounds to identify cystic ovaries. Blood tests include LH, FSH, testosterone, DHEA, insulin, hA1c, estradiol, progesterone and cortisol levels.
For hypothalamic amenorrhea, the workup may include a thorough review of the patient’s medical history, including diet, exercise, and stress levels. Blood tests are conducted to rule out other conditions and measure hormone levels, particularly those associated with the hypothalamus and pituitary gland (like FSH and LH, but also progesterone, estrogen and more.) A lack of abnormal findings, alongside a history of stress or lifestyle factors, often supports a diagnosis of hypothalamic amenorrhea.
Co-occurring Symptoms
Both conditions can present with overlapping symptoms but differ significantly in their manifestations. Women with PCOS often experience weight gain, acne, and hirsutism, along with menstrual irregularities. In contrast, those with hypothalamic amenorrhea often report symptoms such as fatigue, mood changes, and potentially low bone density due to prolonged low estrogen levels. Recent weight loss often accompanies hypothalamic amenorrhea but does not always. Both groups may experience anxiety and depression, often stemming from hormonal imbalances and the stress of managing their symptoms.
Natural Treatment Strategies
Natural treatment strategies are essential for addressing the root cause of both PCOS and hypothalamic amenorrhea. For PCOS, lifestyle modifications, including a balanced diet low in refined sugars, regular exercise, and stress management techniques such as yoga and meditation, improve insulin sensitivity and hormone levels. Supplements like inositol and omega-3 fatty acids may also provide support. In my practice, we start by identifying which type of PCOS a person is dealing with, and putting together a treatment plan from there.
In the case of hypothalamic amenorrhea, we also need to get to the root cause. This may involve reducing stress through mindfulness practices, ensuring adequate caloric intake, and balancing exercise with rest. I often ask my patients to refrain from exercise for a period of time, and include herbal strategies to support stress recovery. Nutritional support, such as incorporating healthy fats and proteins, help restore hormonal balance. In both conditions, fostering a supportive environment and engaging in self-care practices are crucial for recovery.
While PCOS and hypothalamic amenorrhea share some symptoms and are both influenced by stress, they are distinct conditions requiring different approaches to diagnosis and treatment. Understanding these differences empowers you to seek appropriate care and implement effective natural strategies for managing your health.
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I’m Dr. Alexandra MacKillop, a functional medicine physician, food scientist and nutrition expert.
I specialize in women’s health & hormones, addressing concerns like fertility, PCOS, endometriosis, dysmenorrhea (painful periods), PMS symptoms like bloating and mood changes and more.
If you’re looking for a new way to approach your health, I’m here to help you through it. Click to learn more.