top of page

A-Z diagnostic guide for the root cause of thyroid disease

In this guide we will describe what are the tests You can do to find out the underlying cause of Your disease.

Remember that You don't have to do all of these tests. It will depend on the symptoms that You're having, Your past medical history and lab tests that You've already done.

So what is step 1?

First step is testing.


Tests can be divided into few categories. Based on the symptoms You're having and your history of lab tests We can decide which tests are the most important for You. So what should we test for?

  • toxins and triggering medications

  • chronic infections

  • food sensitivities

  • poor stress response

  • intestinal permeability

  • hormonal imbalances

A) Possible Toxins:

Excess Iodine, Fluoride, Medications, Radiation, Petrochemical plants.

Triggering medications:

Iodine, Amiodarone, Fluoride, Lithium, Interferon, Some monoclonal antibodies, Botox, Accutane.

Why excess iodine?

Excess iodine is recognised as an environmental trigger for Hashimoto’s. Most people with Hashimoto’s are actually not iodine deficient.

Which test is the best for iodine deficiency?

The tests are not able to reveal an iodine deficiency or excess, rather they will be reflective of your recent iodine intake.

So how can we know that You're deficient in iodine?

  • having a negative reaction to selenium eating a vegan diet for a long time can predispose

  • eating a diet low in seafood

  • fibrocystic breasts

  • low reverse T3 on a lab test

  • magnesium deficiency

Does it mean nobody should supplement iodine?

No, we're not saying that. Actually around 1/4 of patients will benefit from iodine supplementation.

It's however IMPORTANT to at first asses if You're deficient in selenium or/and If You suffer from gut problem (leaky gut or SIBO). Randomly taking iodine can actually worsen Hashimoto's.

What about the Fluoride?

It appears to have both direct and indirect mechanisms on the endocrine system.

For example, it directly stimulates or inhibits hormonal secretion by interference with second messenger function.

It affects calcium balance and inhibits peripheral enzymes necessary for the activation of the normal hormone action.

Consuming too much fluoride can cause damage to the thyroid gland and production of hypothyroid symptoms.

How to test Fluoride?

You can check your fluoride levels in the plasma. The adverse effects of fluoride are associated with plasma fluoride >4 mcmol/L. However, the optimal levels of fluoride are much lower.

Do we recommend testing for fluoride?

Not really. Why? Because You can simply implement ways to decrease fluoride intake (like water filters) and spend money on other more important testing, which are more beneficial in thyroid disease. Last but not least, fluoride testing is a bit pricy.

How to tell if You may be having too much Fluoride?

- a lot of dental procedures last years

- not using water filters

-living in the "high fluoride" community (South, East, North USA, England, Southern Ireland, Canada, Argentina, North Africa, Northern China, Australia, Brazil, New Zealand, France)

- taking medications that contain fluoride for extended time* **

How to decrease fluoride in the body?

Prevention and detox.

Prevention= water filters + fluoride free toothpaste (

Detox= Liver and gallbladder support (will be posted soon)

What are the triggering medications that are linked to thyroid disease?

- Amiodarone can cause iodine overload even up to 100 times of the optimal daily intake.

It's estimated that up to 25% of the patients who take it, develop thyroid disease, either hyperthyroidism or hypothyroidism.

You may benefit from repeating Your thyroid testing to see if You're reacting to this drug.

If You're reacting, make sure You consult with your doctor eventual change of the anti-hypertensive drug Amiodarone for an alternative.

- Oral estrogen (birth control or hormone replacement therapy):

It causes an increase in thyroxine-binding globulin (TBG).

More TBG in the circulation results in lowered levels of free thyroid hormones in your body.

Furthermore, excess of estrogen, also known as estrogen dominance leads to:

  • hormonal imbalance

  • weight gain

  • inflammation

  • increasemore hypothyroid symptoms

  • worsening of autoimmune condition

- Lithium (used for depression and in bipolar disorder in psychiatry)

Hypothyroidism had been reported in as high as 50 percent of people using lithium carbonate.

However, it's interesting that in hyperthyroidism we can also see deficiency in some patients. This indicates how IMPORTANT this element and drug is for our body.

-Proton Pump Inhibitors (PPI therapy)

Usually used for the treatment of GERD ( gastroesophageal reflux disease), duodenal or stomach (gastric) ulcer or gastritis and indigestion.

The truth is, drugs like omeprazole or pantoprazole have many side effects including: headache, nausea, diarrhea, abdominal pain and gas, anxiety, bone fractures, muscle damage, increased risk of kidney disease, fungus, SIBO, polyps and colitis...

...not to mention decrease of absorption of all vitamins.

Considering thyroid health: PPIs can reduce levothyroxine absorption.

How to avoid using PPIs and find the root cause of Your gut problem?

You can do IgG food sensitivity test and identify foods that induce your reflux.

Furthermore, You can also check for intestinal bacterial overgrowth (SIBO), H.Pylori and nutrient deficiencies.

They're all very often linked to disturbed stomach acid levels.

In case of having one or more of them, You should treat underlying cause and implement natural strategies like apple cinder vinegar, Betaine with Pepsin and gallbladder support.

- Botulinum toxin (Botox)

We do not not recommend its use for cosmetic purposes in thyroid patients. There is a potential link between Clostridium botulinum neurotoxin (botox) and autoimmune thyroid disease.

- Accutane (isotretinoin is a medication used to treat acne)

Studies have concluded that this medication can have a negative effect on autoimmune diseases, diabetes and autoimmune hepatitis. Especially, in genetically-susceptible individuals.

- Interferon (usually used to treat different cancers)

Interferon produced thyroiditis is a significant problem for people who receive IFN therapy. Hypothyroidism is more common ( around 40% of patients) than hyperthyroidism (around 25% of patients).

-Glucocorticoid medications

Can suppress TSH levels.

- Bile acid sequestrant drugs

Usually given to treat high cholesterol. They may reduce the absorption of thyroid medication. Thus, always make sure You at first take care of the gut and liver before giving higher doses of thyroid medication as it can be avoided.

- Sunitinib and Interleukin-2 (used in cancer treatment)

Known to cause hypothyroidism in a subset of patients.

- Some antidepressants

Tricyclic antidepressants and antipsychotic phenothiazines exhibit iatrogenic effects on the thyroid.

-Monoclonal antibodies

Are associated with secondary autoimmune adverse effects including Grave's disease, hypothyroidism, Goodpasture's disease and ITP.

B) Chronic infections

The general mechanism by which these pathogens cause thyroid diseases is via molecular mimicry.

What does it mean? In simple words, your immune system will make a mistake. Instead of attacking only the pathogen, it will start to attack also your organs. In this case the thyroid.

Molecular mimicry is not the only way. Viruses can generate an exaggerated immune reaction that can harm Your thyroid.

EBV specifically can then reside in the thyroid and in doing so it will intoxicate it.

H. Pylori is a bacteria that resides in the stomach, usually between the stomach and the duodenum. It can give symptoms but in most cases it is asymptomatic. If left untreated it can cause severe pathologies, such as Gut Lymphoma. In other H. Pylori is responsible for thyroid diseases due to molecular mimicry.

How to test it?

Stool, blood tests and breath test.

How to treat it? It is a difficult bacteria to eradicate. For this reason your physician can prescribe you a therapy with 4 or 6 antibiotics.

Importantly: when taking antibiotics You must supplement probiotics. You should take antibiotics and probiotics with at least 3h difference between them. You can also try adding natural treatments like apple cinder vinegar etc. but it's very difficult to JUST treat it with natural ways.

EBV (Epstein-Barr virus) is a virus responsible for mononucleosis (aka kissing disease). It is spread through saliva.

Usually our body is able to control it.

However, EBV has been associated with thyroid diseases, like Hashimoto’s.

Why? Because it can reside in the thyroid and generate toxicity.

The immune system will try to destroy it and in doing so it will destroy the thyroid.

How to diagnose it?

Your laboratory test will check for EBV - associated antigens in your blood.

How is it treated? Unfortunately, there is no effective conventional medical treatment.

You must strengthen Your immune system via antioxidants and the right food.

Blastocystosis Hominis is an intestinal parasite. It is surprising very common.

Most of the time it is controlled by the immune system. However, it can give intestinal symptoms diagnosed for IBS, Hashimoto’s and chronic Hives.

Studies showed that this parasite is present in 60% of people with chronic hives. After treatment for Blastocystosis, chronic hives disappeared.

Same as for IBS. Blastocystosis can cause leaky gut. Between 13% to 73% of people Hashimoto’s showed to improve their gut symptoms and thyroid symptoms after treatment.

Blastocystis breaks down secretory IgA, the protective barrier and the immune system of its infected host.

In some patients eradicating the infection lead to Hashimoto’s remission.

How to diagnose it?

GI-MAP: This panel includes bacteria, viruses, opportunistic organisms, normal flora, parasites, and fungi.

The DNA/PCR techniques that are employed by this assessment also measure one’s antibiotic resistance genes and virulence factors that contribute to pathogenicity.

GI pathogen screening with H. Pylori antigen: This panel screens for ova, parasites, bacteria, fungi, yeasts, and occult blood.

It also checks for antigens to Helicobacter pylori, Entamoeba histolytica, Cryptosporidium parvum, and more.

GI effects comprehensive profile: This panel from Genova Diagnostics uses DNA analysis to go beyond the standard parameters for identifying gastrointestinal disorders.

Comprehensive stool analysis: The Comprehensive Stool Analysis evaluates the status of beneficial and imbalanced commensal bacteria, pathogenic bacteria, fungi, and yeast.

How to treat it?

Antiprotozal medications or herbs (The beneficial yeast Saccharomyces boulardii, taken twice per day for at least 30 days).

The use of antiparasitic/anti-yeast herbs such as oil of oregano and berberine.

SIBO, stands for Small Intestine Bacteria Overgrowth.

Reduced motility is one of the risk factors for development of a small intestinal bacterial overgrowth (SIBO). Hypothyroidism is associated with altered GI motility.

In healthy individuals normal small GI motility prevents the overgrowth of bacterial microorganisms.

SIBO is associated with the increase in level of microorganisms above 106 colony-forming units/ml in intestinal aspirate.

This may be associated with colonic-type of bacteria in the small intestine.

Many scientific papers have established that patients with chronic GI symptoms in hypothyroidism should be evaluated for the possibility of SIBO.

Its main symptom is bloating after eating. However, Agassi diarrhoea and constipation are present, sometimes at the same time.

Conditions like IBS, hypothyroidism, fibromyalgia, and restless leg syndrome have all been tied to SIBO.

This condition can cause depletion of vitamin B12, iron and decrease in digestive enzymes that cause Your symptoms.

How to test it?

Breath test.

This is because the breath allows us to determine the presence of gas-producing bacteria. The gas is emitted because of fermenting bacteria, which will usually produce measurable levels of hydrogen and methane.

How to treat it?

You can go for pharmacological, using antibiotics, or herbal (Berberine, oregano, peppermint oil and garlic are all herbal antimicrobials that can help eliminate bacterial overgrowth).

It would also be beneficial if You limit starch, fiber, and the use of probiotics that contain prebiotics like fructooligosaccharides (FOS), inulin, Arabic gum, as well as foods with high prebiotic foods.

There are some diet protocol that can be helpful: the elemental diet, the Specific Carbohydrate Diet, the Low FODMAPS diet, or the GAPS diet.

Candida is a yeast infection that can attack Your intestine.

This yeast can break the intestinal lining and lead to Leaky Gut, and allow for toxins and partially undigested food molecules to cross into the bloodstream.

This will lead to molecular mimicry and development of Thyroid diseases.

History of antibiotics, steroids, pregnancy, recurrent vaginal yeast infections, birth control pills, and a diet rich in simple carbohydrates increases the risk of Candida overgrowth.

The problem is that Candida’s symptoms can cause same symptoms as hypothyroidism.

How to test it?

GI MAP and GI pathogens screen are the best tests to check Candida.

How to proceed?

  1. Starve the yeast by avoiding carbs, mushrooms and alcohol. Follow the body ecology diet for a while until total removal of the yeast.

  2. Use probiotics against yeast overgrowth.

  3. Biotin.

  4. Anti fungal herbs (oil of oregano, colloidal silver, activated charcoal).

  5. Anti fungal medications.

What to do if You are resistant to treatment?

  • test for Blastocystosis hominis

  • heavy metal toxicity

  • mold toxicity

Lyme disease is an infection caused by spirochete bacteria — Borrelia burgdorferi — that is transmitted to people and animals through the bite of an infected deer tick, known as a black-legged tick.

It is described as “multisystem inflammatory disease that affects the skin in its early, localized stage, and spreads to the joints, nervous system and, to a lesser extent, other organ systems in its later, disseminated stages.”

The most distinctive Lyme disease symptom, however, is a skin rash called erythema migrans. This rash usually has a characteristic bulls-eye appearance around the location of the tick bite.

The erythema migrans rash usually occurs in most people in about a week but can extend to a month.

Later on it can give neurological symptoms as well as arthritis like symptoms.

How to diagnose it?

Symptoms and blood work are required.

Blood works are done in a 2 step procedure:

Step 1: The “EIA” (enzyme immunoassay) test or, less commonly, the Immunofluorescence Assay (IFA) is performed.

Step 2: If the EIA or IFA is positive, or inconclusive, the second test performed is an immunoblot test, also known as a “Western blot” test. If the symptoms are new-onset (less than 30 days), the IgM Western Blot is performed.

How to treat it?

Two key antibiotics — amoxicillin and tetracycline — are used to treat Lyme disease.

Typically, a 10-day to a 21-day course is prescribed.

In some cases, the antibiotics cefuroxime or doxycycline are used.

In longer-standing cases of Lyme disease, intravenous (IV) antibiotics are sometimes used, in some cases for a longer period.

How is Lyme disease related to thyroid?

Some patients having Hashimoto’s can have positivity for Lyme disease due to molecular mimicry.

Thus if You tired, in pain, have numbness, headaches, memory problems, pain that changes or moves around the body, symptoms that come and go- no matter what you do, symptoms that worsen around your period, symptoms that get better, or are intensified on antibiotics check Lyme disease. It can be a root cause of your Hashimoto’s!

Yersinia enterocolitica is a bacteria that causes yersiniosis usually caused by drinking contaminated milk or water or eating raw or undercooked meat, usually pork (chitlins). 

Human-to-human infection is possible if the carrier doesn’t thoroughly wash his or her hands before preparing food. You can also get yersiniosis from a blood transfusion.

This bacteria infects the intestines causing diarrhea (usually watery or bloody), vomiting, abdominal pain, and fever which lasts about 4-7 days but can last up to three weeks. 

It then resolves and people believe it is done. This is because this infection can because chronic.

Due to molecular mimicry it can attack the thyroid causing Hashimoto’s or Graves’ Disease.

Infection with the bacterium Yersinia enterocolitica has been implicated in the pathogenesis of Graves' disease since the 1970s (19–21). Y. enterocolitica was shown to contain high-affinity binding sites for the hormone TSH as well as TSHR Abs from patients with Graves' disease (22–24).Jun 1, 2013

There are patients who after treating Yersinia infection had remission.

How to diagnose it?

Blood tests are more reliable. You tests for IgA, IgG and IgM.

IgG +ve equal past infection

IgG and IgM +ve equal infection present for 1-3 months.

IgG and IgA +ve but IgM-ve then the infection has been going on for more than 3 months.

You can also check the stool.

If the infection does not resolves by itself then You will have to use antibiotics.

It is possible that the Yersinia enterocolitica blood test may cross-react with a virus or the bacteria Borrelia burgdorferi which causes Lyme disease. 

If you use an effective treatment for Yersinia and then retest the blood and it is still showing active infection, this may mean that the positive test was actually for a virus or Lyme disease.

If Yersinia comes back positive in a stool analysis, then the lab will run a sensitivity to identify herbal medicines that will eradicate the bacteria. 

Berberine, black walnut, caprylic acid, oil of oregano, uva ursi, grapefruit seed extract and silver can all eradicate this bacteria. 

The sensitivity test will tell you which one of these will work best.

Something a combination of all for 4 weeks is necessary and sufficient to eradicate the infection.

C) Food Sensitivities

Food sensitivities are usually testes with the IgA, IgM and IgG testing. The common symptoms in patients who are sensitive to one food or other are: bloating, acid reflux, irritable bowel syndrome, joint pain, anxiety, palpitations or anxiety.

What are the most common ones?

- gluten

- dairy


Why is it important to determine if you have problem with gluten?

- Eliminating gluten from diet may have positive effect on Your gut health, which will improve conditions like Hashimoto's thyroiditis, skin conditions, weight gain, constipation, depression and many others.

- Gluten can be problematic for those who DO NOT have celiac disease (non-celiac gluten sensitivity).

- 90% of the patients with thyroid disease will benefit from eliminating gluten

WHY allergy and food intolerance tests can be worthless and waste of money?

- Food allergy tests are questionable because they only test for IgE. You may be having a food intolerance, which involves also IgA, IgM and IgG antibodies.

- That's why the best test is simply an elimination diet. Testing is not always accurate. Around 50% of the time the food allergy test says that certain food is ok, even though the patient reacts to it. This is very disappointing after spending 400-700$ on an allergic test.

Which diet will work best when You have a lot of food sensitivities?

- AIP (autoimmune protocol diet) for at least 90 days

- If AIP works, then You can transition to Paleo or Keto diet

- If AIP does not work, You should further eliminate oxalates and histamine rich food

D) Poor stress response

There are 4 available methods of testing Your cortisol level:

  • Saliva testing

  • Urine testing

  • Blood testing

  • ACTH Stimulation test (STIM)

We went more in details with this in this article:

E) Intestinal permeability

Most people with Hashimoto’s and Grave's disease have problems with leaky gut and/or SIBO to some extent...

and even if You don't have any gastrointestinal symptoms, You may still have leaky gut or SIBO.

By reversing these conditions, your autoimmune status should greatly improve.

An unhealthy gut lining may have holes in the lining, allowing partially digested food, toxins, and bugs to enter the tissues beneath.

This may trigger inflammation and changes in the gut flora.

Modifications in intestinal bacteria (gut dysbiosis) and inflammation can lead to the development of chronic diseases like Hashimoto's disease and Graves' disease.

What causes leaky gut?

- nutrient deficiencies

- intestinal infections

- gut bacteria imbalance

- chronic stress

- deficiencies in stomach acid and digestive enzymes

- food sensitivities

F) Hormonal imbalances

The most common one is definitely problem with estrogen (estrogen dominance).

𝐇𝐨𝐰 𝐭𝐨 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐲 𝐟𝐫𝐨𝐦 𝐥𝐚𝐛 𝐭𝐞𝐬𝐭𝐬?⁣

- 𝘕𝘰𝘳𝘮𝘢𝘭 𝘴𝘦𝘳𝘶𝘮 𝘦𝘴𝘵𝘳𝘰𝘨𝘦𝘯 + 𝘭𝘰𝘸 𝘴𝘦𝘳𝘶𝘮 𝘱𝘳𝘰𝘨𝘦𝘴𝘵𝘦𝘳𝘰𝘯𝘦⁣

- 𝘕𝘰𝘳𝘮𝘢𝘭 𝘴𝘦𝘳𝘶𝘮 𝘦𝘴𝘵𝘳𝘰𝘨𝘦𝘯 𝘭𝘦𝘷𝘦𝘭𝘴 + 𝘯𝘰𝘳𝘮𝘢𝘭 𝘴𝘦𝘳𝘶𝘮 𝘱𝘳𝘰𝘨𝘦𝘴𝘵𝘦𝘳𝘰𝘯𝘦⁣

- 𝘏𝘪𝘨𝘩 𝘴𝘦𝘳𝘶𝘮 𝘦𝘴𝘵𝘳𝘰𝘨𝘦𝘯 + 𝘯𝘰𝘳𝘮𝘢𝘭 𝘴𝘦𝘳𝘶𝘮 𝘱𝘳𝘰𝘨𝘦𝘴𝘵𝘦𝘳𝘰𝘯𝘦 ⁣

- 𝘗𝘳𝘰𝘨𝘦𝘴𝘵𝘦𝘳𝘰𝘯𝘦 𝘳𝘦𝘴𝘪𝘴𝘵𝘢𝘯𝘤𝘦 𝘴𝘺𝘯𝘥𝘳𝘰𝘮𝘦 (𝘰𝘷𝘦𝘳𝘢𝘭𝘭 𝘳𝘦𝘥𝘶𝘤𝘵𝘪𝘰𝘯 𝘪𝘯 𝘵𝘩𝘦 𝘭𝘦𝘷𝘦𝘭𝘴 𝘰𝘧 𝘱𝘳𝘰𝘨𝘦𝘴𝘵𝘦𝘳𝘰𝘯𝘦 𝘳𝘦𝘤𝘦𝘱𝘵𝘰𝘳𝘴)⁣

𝐇𝐨𝐰 𝐭𝐨 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐲 𝐟𝐫𝐨𝐦 𝐬𝐲𝐦𝐩𝐭𝐨𝐦𝐬? ⁣

- Reduced metabolism ⁣

- Fatigue/ lack of energy⁣

- Problem with Bowel movements ⁣

- Changes to Your mood: depression, feeling down⁣

- Anxiety⁣

- Problems with fertility ⁣

- Hair loss or Thinning Hair⁣

- Changes to Your menstrual cycle⁣

- Weight gain ⁣

- Decreased libido ⁣

- Breast tenderness ⁣

- Water retention in feet or face ⁣

- Poor quality of sleep⁣

Testing for progesterone and progesterone to estrogen ratio is also beneficial. Testosterone is also useful to asses if You have optimal levels of this hormone.


1,093 views0 comments


bottom of page