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A Functional Medicine Approach to Amenorrhea: A Case Study

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A Functional Medicine Approach to Amenorrhea: A Case Study

1 in 25 women experiences amenorrhea at some point in their lives. Amenorrhea is a medical condition characterized by the absence of menstruation. It can be caused by a range of physical and psychological factors and can significantly impact a woman's physical and mental health. Treatment for amenorrhea will depend on the underlying cause and may involve lifestyle modifications, hormonal therapy, or other medical interventions.


CC: Amenorrhea, Weight Gain, Fatigue

Sophie is a 21-year-old woman who presented to my office for a functional medicine evaluation of new weight gain, chronic inability to lose weight, and cessation of her menstrual period. Her periods were previously regular, approximately every 28 days, lasting 4-5 days since menarche at age 12. Two years prior to our visit, she began skipping periods and had not had a period in six months. She denied the use of oral contraceptives or exogenous hormones. She denied symptoms of excess testosterone such as facial hair growth, male pattern baldness, or acne. She noted fatigue, particularly in the morning at the end of the day, difficulty falling asleep at night, and frequent waking.

Her new rapid weight gain over the past 18 months was also concerning. At the time of our visit, she weighed 250 pounds at 5’11 inches tall. Her goal weight was 150 pounds. She stated that she was slightly overweight as a child from ages 8 to 10. Her weight normalized during puberty, and she lost weight from ages 11 to 13, but then slowly gained weight from age 15 to present with more rapid weight gain in the past 18 months. She reported success with a low carbohydrate, gluten-free, anti-inflammatory eating plan at age 17. She lost 30 pounds, but she gained it back after stopping this meal plan.

She noted that dairy caused bloating and nasal congestion issues, but she ate it regularly. She stated she felt better if she ate small meals but craved sweets and found it hard to avoid them.

She was not currently exercising but was physically active with household work and gardening throughout the day. She worked for her family farm and had ongoing exposure to pesticides. She noted a family history of Hashimoto’s thyroiditis in her mother and maternal grandmother. Prior to seeing me, another provider prescribed adrenal support and gut-healing supplements based on labs showing high cortisol and gut dysbiosis. She had not improved her symptoms with this regime for six months.


Suspected Diagnosis

Based on her symptoms, I requested extensive laboratory work, including a full thyroid panel, nutrient levels, hormone levels, and blood sugar markers. Her sudden loss of period that coincided with weight gain made me suspect polycystic ovarian syndrome (PCOS).

PCOS is a complex hormonal condition diagnosed by the presence of two out of three of the following: multiple cysts on the ovaries, irregular periods, and elevated androgens.

PCOS is characterized by dysfunctional glucose metabolism with insulin resistance and often elevated blood sugar. Elevated insulin is thought to drive high androgens. Though the cause of PCOS is multifactorial and can include a combination of genetic predisposition, chronic inflammation, exposure to chemicals or hormones, metabolic dysfunction, dietary factors, disruption in the gut microbiome, impaired detoxification, glucose, and insulin dysregulation must be addressed to achieve hormonal balance.

Initial Laboratory Findings


Based on her extensive lab panel, we were able to conclude the following underlying issues that were potentially contributing to her amenorrhea and weight gain:

  • Hashimoto’s Thyroiditis: Due to elevated antibodies with underactive thyroid function due to high TSH and suboptimal free thyroid levels and high reverse T3. Elevated reverse T3 impairs the conversion, binding, and effectiveness of T4 to T3. A thyroid ultrasound showed diffuse thyroid swelling with no nodules.
  • Polycystic Ovarian Syndrome: Suspected with high insulin, high blood sugar, high testosterone, low progesterone, and low SHBG. This was confirmed with pelvic ultrasound showing the presence of multiple cysts on both ovaries.
  • Dyslipidemia/Elevated tTriglycerides: contributing to her metabolic dysfunction.
  • Non-Alcoholic Fatty Liver Disease: Characterized by high AST, high ALT, and dyslipidemia. Liver ultrasound ordered but not completed.
  • Hyperparathyroidism due to high PTH and high calcium: Sophie was referred for endocrinology evaluation and underwent surgical removal of parathyroid adenomas. Calcium and PTH were regulated after surgery, but this did not affect her weight or amenorrhea.
  • Low progesterone: We were unsure where she was in her cycle due to her amenorrhea but approximated that her LH and FSH were more consistent with luteal phase readings. Using this estimate, we determined that her progesterone was also low. Progesterone is essential for normal ovulation and plays a role in healthy metabolism through interplay with thyroid hormones.
  • Vitamin D deficiency: Optimal levels can improve insulin sensitivity and hormone signaling. This was addressed with endocrinology also as part of management for her hyperparathyroidism.
  • Elevated ferritin due to high levels with normal iron and TIBC levels. Additional labs ruled out the presence of genetic hemochromatosis and ferritin levels normalized with functional medicine treatment.

Functional Medicine Approach: Initial Plan

Sophie was placed on a low carbohydrate, grain-free, dairy-free food plan designed for insulin resistance and PCOS. I asked her to avoid grains and dairy due to potential cross-reactions with food antibodies perpetuating her autoimmune thyroid process. She was also encouraged to incorporate intermittent fasting for 16 hours per day and eating within an 8-hour window to help lower her insulin. Because of her young age, she wanted to avoid thyroid medication, so she started a comprehensive thyroid supplement with nutrients for thyroid health, including selenium, iodine, zinc, and ashwagandha, to improve T4 to T3 conversion.

She was prescribed a combination supplement with berberine, alpha-lipoic acid, chromium, and cinnamon to help with insulin resistance. She was also prescribed myo-inositol and d-chiro inositol for ovarian support, insulin sensitivity, and lower androgens.

To help support her body’s ability to detoxify excess hormones, she used a protein shake designed to support all liver phases of detoxification. She used this as a meal replacement for 1-2 meals a day for three weeks, then daily with her low carb meal plan.

Appropriate referrals and tests were made for hyperparathyroidism, fatty liver, and suspected hemochromatosis. She was encouraged to begin a regular exercise regime, including walking and gradually building to a more intense regimen as tolerated. Exercise further helps with insulin sensitivity and raising HDL.

Lastly, she was prescribed topical progesterone cream 40 mg for 14 days per month to address low progesterone levels. We also reviewed the use of Vitex/Chaste Berry, but her mother also had a history of low progesterone at a young age and urged her to use the topical cream first.

First Follow Up: 4 Weeks From Initial Consultation

One month later, she noted a weight loss of 5 pounds. She was doing well with her diet and reported an improvement in bloating and sinus congestion with dietary changes. She found it challenging to adhere to her meal plan when traveling away from home but was consistent 80% of the time. She was walking daily for 45 minutes and added jumping jacks. Her energy had improved, and she had noticed some mid-cycle spotting but not a full menstrual period this month.

Second Follow Up: 8 Weeks From Initial Consultation

At our next follow-up, she noted an additional weight loss of 6 pounds that month for a total weight loss of 11 pounds in two months. She continued to note improvements in her sleep and energy. She adhered to her diet 90% of the time and exercised most days. She found the progesterone cream was helping her sleep and had been using it nightly. However, she had no spotting this month. I recommended she return to using her progesterone cream for only 14 days per month as prescribed to mimic a natural cycle better. We also doubled her myo-inositol ovarian supplement. Lastly, she was prescribed a fasting-mimicking diet for five days with the option to repeat monthly for three months to further help with her insulin resistance and PCOS.

Third Follow Up: 12 Weeks From Initial Consultation

At our third follow-up, she had reported a total weight loss of 20 pounds. She successfully completed one five-day cycle of a fasting-mimicking diet and felt well on this. Her labs showed improvements in blood sugar, cholesterol markers, and her testosterone, TSH, and thyroid antibodies were trending down. She had some mid-month spotting again but did not have a full period. At this visit, we reviewed additional hormone testing options, including a Rhythm Plus test from Genova Diagnostics to look at her estrogen and progesterone levels throughout the whole month and determine if additional support was needed.

We also discussed GI Map stool testing to determine if underlying gut issues needed to be addressed, such as increased intestinal permeability or dysbiosis, to balance her hormones further. She declined these tests at this time. Between her third and fourth follow-up, her entire family completed a comprehensive six-day detox plan with protein shakes, lymphatic drainage support, probiotics, and gut support. She noted having excellent mental clarity and energy during this detoxification and lost additional weight.

Fourth Follow Up: 16 Months From Initial Consultation

Sophie traveled internationally for one year. During this time, she was unable to take her supplements regularly, adhere to the diet plan, or exercise consistently. Her weight had increased, and she had ceased having any spotting. Her labs had reverted to pre-treatment levels.

We reviewed the most effective elements of her treatment plan over the past 16 months, including her low-carb diet, myo-inositol, progesterone cream, thyroid support, and periodic fasting diet /detox diets. At this time, she did not want to do any additional testing or start thyroid medication.

She is once again traveling internationally but took supplements with her and plans to try to adhere to a low carbohydrate, anti-inflammatory diet. We will follow up in 6 months when she is home.


This case illustrates the many complex factors contributing to amenorrhea and weight gain. In Sophie’s case, her Hashimotos and PCOS were addressed and required ongoing treatment and support to prevent a worsening of her symptoms. Though she is not completely healed, she has made tremendous progress with her weight and restarting her cycle but requires consistency in her regime and additional support.

Additional laboratory work that will be helpful in Sophie’s case in the future includes stool testing to assess for dysbiosis and inflammation, cycle mapping hormone testing to determine her hormone levels throughout the month, and additional testing for environmental toxins, including mold, heavy metals, and pesticides based on her favorable response to detoxification protocols and environmental exposures.

This case also underscores the importance of comprehensive endocrine testing with these complex cases and appropriate collaboration with specialists as we were able to identify and treat her underlying parathyroid condition.

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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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