The autoimmune thyroid, post-partum & hormone connection


As a Naturopathic Doctor and functional medical practitioner with a passion for thyroid health I diagnose and treat a lot of thyroid imbalances in my practice. The thyroid plays an important role in fertility and pregnancy, and is often overlooked. Ninty percent of thyroid conditions are caused by autoimmunity 1 and the immune system is influenced by hormones. Immune cells have hormone receptors on them, and hormones can up regulate or down regulate the immune system. Testosterone, estrogen, progesterone and the stress hormone cortisol all interact with the immune system. Overall testosterone and estrogen are anti-inflammatory which means they are going to calm the immune system down. Cortisol has immune calming and suppressing action. For example, we often get sick after a stressful time, our immune systems have been suppressed and vulnerable to exposure but unable to mount a response. Once you finally get that holiday at the end of exam time, your immune system comes back to life and mounts a response resulting in you feeling sick.

Why are women more likely to get autoimmune conditions? 

Women are more likely to get autoimmune conditions then men, in fact women make up 75% of those with autoimmunity 2. Women have more estrogen then men, and estrogen is suppose to be anti-inflammatory so what the heck? Well, we often see autoimmunity rear it’s ugly head when estrogen and cortisol are low. For example estrogen soars during pregnancy and autoimmune symptoms generally improve, and many women are diagnosed with autoimmune conditions after pregnancy.  That post-partum time when our adrenals are burnt out, our estrogen is low, the immune system flares up, attacks the thyroid and causes hypothyroidism or other autoimmune conditions. Similarly autoimmune symptoms can be worse on mensuration when estrogen and progesterone are at their lowest. 

Another very common time to see the onset of an autoimmune condition is after a period of stress. The stress system, regulated by the hormone cortisol, plays an integral role in hormone production in the body. When men and women go through prolonged periods of stress the adrenals burns out.  During burn out we don’t have enough cortisol to help calm the immune system when it acts in an abnormal way, like attacking its own tissues as seen in autoimmunity. Low cortisol also drains our sex hormones, when cortisol is low the body shunts all the its hormone making resources towards restoring cortisol, leaving very little resources for making the anti-inflammatory hormones estrogen, progesterone, and testosterone. Ever wonder why your libido drops when your stressed out? Cortisol is draining your sex hormone testosterone. 

What does this mean for Post-Partum women? 

It means post-partum can be a very difficult time!  If an autoimmune thyroid condition like Hashimotos kicks in after pregnancy, you are more likely to gain weight, feel depressed and have low energy. Layer this on top of sleep deprivation and huge fluctuation in hormones, and life is going to be a challenge. It can take months even years to recover with out the proper support. 

What type of screening test can be done to find out if you have an autoimmune thyroid condition? 

Most doctors only run TSH, this is not sufficient!! This is why many autoimmune and thyroid conditions go undiagnosed until you are feeling really sick. If you want to get an idea of what your thyroid is doing or if you have an autoimmune thyroid condition you need to see more then TSH. You want to evaluate how your thyroid is producing thyroid hormones, how your body is activating inactive T4 into active T3 and you want to see if the immune system is producing anti-bodies against your thyroid. To evaluate this you need the following tests:

Hypothyroid symptoms, Hashimoto’s thyroiditis, natural treatments, alternative therapies, hypothyroid

  • TSH
  • Free T3
  • Free T4
  • Reverse T3
  • Thyroperoxidase antibodies (Anti-TPOs)
  • Thyroglobulin antibodies (Anti-TG’s)
  • Oral temperature
  • Testosterone
  • Estradiol
  • Day 21 Progesterone
  • Salivary Cortisol


Take 12 temperature readings with a digital or shake down thermometer at 11am, 3pm, and 6pm. If your average oral tempurature is below 98.6F, your not getting enough T3 into your cells. And this can have you feeling terrible.

As we have seen the immune system is dynamic, interacting with other hormones, and your body is a complex and interconnected web of beauty. Evaluating other hormones is, in my opinion, a must to get the bigger picture of what’s going on. Evaluating your adrenal stress system with a four point salivary test, and looking at your sex hormones can be done in urine or blood. 

What are the treatment options?

As a Naturopathic doctor, we take all these pieces and put it together for you, stress, diet, hormones, and even your spirituality. As I mentioned we are beautiful dynamic beings, our bodies are the most amazing and complicated things. You can’t just throw a drug like Synthroid at everyone with hypothyroidism or corticosteroid at all autoimmune conditions and expect them to feel great, not alone heal themselves. You can heal yourself, you can heal your thyroid and your immune system. The sooner you catch it the better. Don’t wait until the immune system has damaged your thyroid beyond repair.  Remember Hashimoto’s and Grave thyroid conditions are not primarily a thyroid problem. They are an immune problem! 

We take an integrative approach, balance your thyroid so you can start feeling energized and healthy. We balance your immune system so your thyroid can start to repair itself. We correct the diet and improve the gut so the immune system isn’t being fueled in the wrong way. We balance your hormones so your immune system responds and regulates in a healthy way, and help your stress system come back to life.  If you are considering getting pregnant, then you will want to get your adrenal and immune health in order first so you can feel vital and healthy through and beyond pregnancy. 

Sounds like a lot? Yes, healing yourself is a journey. With the right support you get through, you feel better, and you can be vibrant for your family. 

Diet recommendations for a healthy immune system:

Avoid the major allergens until you know which ones are problems for you- corn, gluten, dairy, eggs, tree nuts, peanuts, soy, and shellfish are the biggest ones. 

Increase anti-oxidant rich foods, berries, dark leafy greens, Try including a green juice daily, or adding super-greens powder to your smoothie. 

Get enough iodine and selenium, Brazil’s nuts are rich in selenium, seaweed is rich in iodine. 

Cut out gluten! If you do nothing else with an autoimmune condition this one is crucial. 

Fasting. Fasting has been shown to turn around autoimmune flare ups. Water fasting, the Fasting Mimicking Diet, and juice fasting (low sugar juice only) for 3-5 days. Best done under supervision of a qualified Naturopathic Doctor and not during pregnancy. 

Cut back on the sugar! Sugar is fuel for all things bad in the body. Seriously do it! 


1. Amino N., (1988). Autoimmunity and Hypothyroidism.   Aug;2(3):591-617.

2. Franco JS, Amaya-Amaya J, Anaya JM., (2013). Thyroid Disease and Autoimmune DiseaseFrom Bench to Bedside [Internet]. Bogota (Colombia): El Rosario University Press;  Jul 18. Chapter 30.

3. Fairweather, D., Frisancho-Kiss, S., & Rose, N. R. (2008). Sex Differences in Autoimmune Disease from a Pathological Perspective. The American Journal of Pathology, 173(3), 600–609.