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A Functional Medicine Protocol for Amenorrhea

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A Functional Medicine Protocol for Amenorrhea

During a woman's reproductive years, having a regular period is a sign of her overall health and well-being. Missing your period during these years could indicate pregnancy, breastfeeding, menopause, or various health concerns. Missing your period is medically referred to as amenorrhea and, in the absence of pregnancy, should be taken seriously and should be investigated.

In this article, we will shed some light on the different types of amenorrhea, what can cause it, functional laboratory testing to uncover a root cause, as well as various conventional and functional medicine treatment options.

What is Amenorrhea?

During reproductive years, a woman has her menstrual period once approximately every 28 days, which is the length of her menstrual cycle. A series of hormone changes occur every month to prepare the body for a potential pregnancy. If pregnancy doesn't happen, a shedding of the uterine lining occurs during the menstrual period.

Amenorrhea is the absence of menstrual periods in women of reproductive age. Amenorrhea is not a disease, and there are certain times during a woman's reproductive years when amenorrhea is actually normal, including during pregnancy, postpartum, or while breastfeeding. Amenorrhea can be classified as either primary or secondary.

Primary amenorrhea is when menstruation has not yet occurred in a female by age 15, despite normal growth and development of secondary sexual characteristics like breast development and pubic hair growth.

Secondary amenorrhea is when a woman who previously had regular menstrual cycles stops having periods for three or more months or six months or more in women who previously had irregular periods.

What Causes Amenorrhea?

Reproduction is an energetically demanding process, and when the body is under significant stress, certain defense mechanisms in place de-prioritize reproduction. Stressors such as eating disorders, weight loss, excessive exercise, or severe physical or psychological stress suppress the hypothalamic-pituitary-ovarian (HPO) axis, which is the communication network of hormones between these endocrine glands that regulate the reproductive process. The suppression of this axis can lead to primary or secondary amenorrhea and is called Functional Hypothalamic Amenorrhea (FHA). The most common triggers for FHA are psychological stress, excessive exercise, and nutritional deficits, such as burning more energy than you take in.

Other factors which may increase the risk for amenorrhea include a family history of amenorrhea or early menopause, as well as genetic changes.

Various factors, including abnormal pelvic anatomy, chromosomal abnormalities, and problems with the hypothalamus or pituitary gland can cause primary amenorrhea.

As we know, it's normal for a woman not to experience a menstrual period during pregnancy. This is the most common cause of secondary amenorrhea. Additional causes of normal secondary amenorrhea include breastfeeding and menopause.

However, secondary amenorrhea can also stem from other causes, which may include:

  • Certain birth control methods (Depo Provera, intrauterine devices (IUDs), and some birth control pills)
  • Certain medications (antipsychotics, antidepressants, blood pressure, and allergy meds)
  • Cancer treatments (chemotherapy and radiation)
  • Uterine surgeries that cause scarring, or removal of the ovaries or uterus
  • Primary ovarian insufficiency (experiencing menopause before the age of 40)
  • Pituitary disorders (tumors or increased prolactin production)
  • Obesity
  • Inadequate nutrition (including nutritional deficiencies or relative energy deficiency in sports (RED-S))
  • Hormonal dysfunction (such as Polycystic Ovarian Syndrome (PCOS), hypothyroidism, and adrenal disorders)
  • Ovarian tumors
  • Chronic illness

Functional Medicine Labs to Test for Root Cause of Amenorrhea

The first step in assessing for a root cause of amenorrhea is a pregnancy test since it's the most common cause of secondary amenorrhea. A physical examination and pelvic exam help identify scar tissue or tumors and indicate whether additional imaging may be necessary to evaluate these possibilities further.

Your Functional Medicine practitioner will also order various functional laboratory tests to determine the underlying root cause of your amenorrhea.


A Micronutrients Test will help identify whether any nutritional deficiencies are driving your amenorrhea. This particular test from SpectraCell Laboratories is very thorough. It measures 40 different vitamins and minerals, amino acids (the building blocks for protein), and fatty acids (including omega-3 fats which are important for hormone health), providing an excellent look into your nutritional status.

Female Hormones

The DUTCH Plus™ test provides helpful information about sex hormones to determine whether your amenorrhea may be caused by dysfunction in the hormone signaling between your brain and your ovaries or the HPO axis. This test also measures androgen hormones, which can indicate whether PCOS may be a factor.

Analysis of prolactin levels will help determine whether there are problems with your pituitary gland causing your amenorrhea.

Adrenal Hormones

The DUTCH Plus™ test mentioned for female hormone testing also evaluates adrenal hormones, which is a helpful way to identify whether issues with the body's stress hormones or the hypothalamic-pituitary-adrenal (HPA) axis are contributing factors.

Thyroid Hormones

Testing thyroid hormones is important in evaluating amenorrhea because abnormal thyroid hormone levels can play a role in the root cause of amenorrhea, and may also impact prolactin levels.

Blood Workup

A comprehensive blood workup, including CBC, CMP, hemoglobin A1c (HbA1c), insulin, and iron panel, helps assess overall health and rule out underlying health conditions (such as PCOS or chronic illnesses) that could be contributing to amenorrhea.

Conventional Treatment for Amenorrhea

Sometimes, a combination of conventional treatments and functional medicine support may be necessary to address your healing journey properly. Conventional treatments may include:

  • Surgery to address anatomical abnormalities, scar tissue, or tumors
  • Hormone therapy, including birth control pills or hormone replacement therapy (HRT) to reinitiate menstruation
  • Thyroid hormones to address thyroid conditions

Functional Medicine Amenorrhea Protocol

A Functional Medicine protocol for amenorrhea involves a targeted and unique approach for you based on your history, examination, and functional laboratory testing to identify a root cause. A well-rounded approach includes healthy lifestyle practices, supplements, and other therapies to support you in restoring your hormone health.

Lifestyle Changes for Amenorrhea

As with most aspects of life, balance is key. Finding a balanced approach to exercise and physical activity to support a healthy return of your period depends on your root cause for amenorrhea. Those with obesity and PCOS may benefit from various types of regular physical exercise, including aerobic, strength training, and yoga. Those with inadequate nutritional support, excessive exercise regimens, or having a root cause associated with FHA may benefit from decreasing physical activity or taking a more balanced approach to their movement practices to support better hormone health.

If psychological stress or eating disorders are a root cause of your amenorrhea, talk therapy is an invaluable tool to support your healing journey. If you're struggling with FHA, Cognitive Behavioral Therapy (CBT) is a type of talk therapy you may find helpful.

Prioritizing sleep and engaging in other forms of stress management, such as yoga and meditation, are also amazing ways to support you on your path to better health as they have been shown to improve stress hormones and inflammation. Engaging in activities that stimulate the Vagus nerve, a cranial nerve important in the body's resilience, is another way to stimulate the body's relaxation response when stress is a root cause.

Nutrition for Amenorrhea

A balanced nutritional approach for supporting a healthy menstrual cycle considers the causative factors. If excessive exercise, inadequate caloric intake, and nutritional deficiencies are factors, a balanced nutritional approach would focus on adequate protein and healthy fat intake and a diet high in vitamins, minerals, and phytonutrients to meet your body's energy and nutrient demands.

If obesity, PCOS, or other metabolic imbalances are a factor, a balanced nutritional approach would include a focus on low-glycemic foods and a diet known to benefit healthy blood sugar balance, such as the Mediterranean Diet.

A balanced approach to nutrition also factors in the results of a micronutrient test to ensure you focus on foods high in the nutrients you are showing deficiencies or insufficiencies.

If your micronutrient test uncovers any deficiencies or insufficiencies, your Functional Medicine practitioner will suggest foods that are high in those micronutrients to ensure you have a well-rounded nutrition plan to support your best health.

Supplements for Amenorrhea

Your Functional Laboratory tests will indicate which specific vitamins, minerals, or herbal supplements will be supportive of your hormone health.

Various herbal supplements are shown to be beneficial for the different hormone imbalances that can cause amenorrhea. Ashwagandha is an herb that can benefit both thyroid and adrenal hormone imbalances, supporting the HPA axis and better sleep and resilience. Chasteberry can be helpful for PCOS and supporting balance in female hormones, and fennel tea has been shown to restart menstrual periods in women with amenorrhea.


Your menstrual cycle is a valuable indicator of your hormone health and overall well-being. Missing a menstrual period can signal a normal reason for amenorrhea, such as pregnancy, breastfeeding, or menopause. But, it can also be an important indicator of imbalance and dysfunction in the body.

If you have regular cycles and miss a period for more than three months, or if you have irregular periods and miss a period for six months, you should seek the care of a Functional Medicine practitioner to identify why you've stopped menstruating normally.

A Functional Medicine approach to restoring menstruation and supporting overall health may include a combination of conventional and functional medicine treatments. A personalized, well-rounded plan will incorporate a balanced approach to exercise and nutrition and ensure stress management is appropriately addressed to support your best health.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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