Finding Your Root Cause: Key Lab Tests

I receive so many questions from my readers about which labs to get for Hashimoto’s and where to get them. Figuring out which tests you should do can be overwhelming because there’s quite a bit of information out there, and there are multiple tests that can give us an idea of our current thyroid function, as well as triggers that can reveal why the thyroid may be malfunctioning. I wrote this article in hope that it serves as a starting point to help you determine which lab tests will be most helpful for uncovering your triggers.

I highly recommend working with a Functional Medicine clinician on your thyroid journey. Functional Medicine is a medical specialty dedicated to preventing, finding, and treating underlying causes of chronic illness, rather than merely treating disease symptoms.

If you have a practitioner who is willing to work with you, that practitioner can order most of the tests listed here. If you don’t have a practitioner like this on your team, I’ve spent some time reaching out to various lab companies to set up specialized channels that will allow you to self-order your own labs at a discount. I’ll specify which tests are usually covered on insurance if you have a willing practitioner that can bill insurance, which tests can be self-ordered and then submitted to insurance, and which ones are usually an out-of-pocket expense that you may need to save for. (You can use Health Savings Accounts for most.)

In this article, I will go over the tests that I think are critical for finding the root cause(s) of your Hashimoto’s condition, including:

• Thyroid testing
• Nutritional testing
• Adrenal testing
• Gut health testing
• Infections testing
• Genetic testing

Comprehensive Thyroid Testing

Establishing a baseline for your thyroid health and testing on a regular basis is a crucial first step in monitoring your health and understanding how possible “root cause” triggers may be affecting you. If you haven’t had any of the following thyroid tests done in the last three months, I recommend having them done as soon as possible.

TSH Test

TSH is a pituitary hormone that responds to low and high amounts of circulating thyroid hormone. This lab test reveals elevated TSH in people who have advanced Hashimoto’s or primary hypothyroidism. However, levels of thyroid hormone can fluctuate, so this test can potentially be misleading. It’s important to note that some people with Hashimoto’s and central hypothyroidism might have a normal reading when tested. People with Graves’ disease generally have a low TSH.

You can often predict an eventual rise in TSH decades before it happens. Usually, there’s an elevation in thyroid peroxidase antibodies (TPO Antibodies) and Thyroglobulin Antibodies (TGAb Antibodies) before TSH goes up. Those with Graves’ disease or thyroid cancer can have elevated thyroid antibodies, including TPO, TGAb, and TSH receptor antibodies.

The TSH level considered “normal” has been skewed for years because the original data collected included elderly patients and people with compromised thyroid function. Although there is an updated range, many doctors have been slow to join in. This is why I encourage you to work with a functional medicine doctor that will treat you and not just your labs.

Functional medicine practitioners have further defined that normal reference ranges should be between 1 and 2 μIU/mL, for a healthy person not taking thyroid medications. Anecdotally, most patients feel best with a TSH between 0.5-2 μIU/mL.

The TSH test can be useful in optimizing thyroid function by ensuring the TSH levels stay within the optimal reference range while implementing lifestyle interventions and medication dosage changes.

Free T4 and Free T3 Tests

Doctors usually measure total T3 and T4, which can be misleading because T3/T4 hormones are often bound to different types of proteins and aren’t available for proper use in our body. T4 (thyroxine) and T3 (triiodothyronine) are the two main thyroid hormones. T4 is known as prohormone and is 300 percent less biologically active than T3. T3 is the main biologically active thyroid hormone that runs our metabolism and gives us beautiful hair and energy.

Most of the commonly prescribed thyroid medications, like Synthroid (levothyroxine), only contain T4 and need to be converted to T3 in the body. In theory, the T4 to T3 conversion works as it’s supposed to, but in reality, we may not always convert T4 to T3. Free T4 and Free T3 tests reveal the levels of available and free thyroid hormones that interact with thyroid receptors.

Some clinicians may only test for free T4, but free T3 is also important to test, as some individuals may not be converting the T4 to the active T3 hormone properly. Thus, people may have normal T4 levels, but low T3 levels.

Thyroid peroxidase (TPO) and Thyroglobulin (Tg) Antibodies Tests

The TPOAb and TgAb tests measure the antibodies that are the markers of autoimmunity, letting us know that the immune system is launching an attack on the thyroid gland. Generally, the higher the thyroid peroxidase and thyroglobulin antibody numbers, the more aggressive the autoimmune attack is on the thyroid. However, not everyone will have antibodies. (Read more about how some people with Hashimoto’s may not have any antibodies.) While not everyone with Hashimoto’s will have these antibodies, those that do can use them as a gauge of how aggressive the attack is on their thyroid, and can track the antibodies over time to see if their current lifestyle interventions are working. A reduction in thyroid antibodies is usually an indication that their lifestyle changes are helping.

Thyroid Ultrasound

An ultrasound reveals what’s happening with your thyroid. It shows whether or not you have changes consistent with Hashimoto’s, which could be characterized by changes in blood flow to the thyroid gland, a shrunken or enlarged thyroid, or even a “rubbery” thyroid. If you have nodules present, then they need to be watched, and an ultrasound can spot tumors that need to be biopsied or examined. (You can read more about diagnosing thyroid cancer here.)

I recommend doing an ultrasound at least once in your lifetime. If there are issues that need monitoring, then it’s recommended to have the ultrasound done routinely, such as on an annual basis. If everything stays consistent with Hashimoto’s, you should probably have one done every five years. If you’re actively trying to regenerate thyroid tissue and are doing thyroid regeneration protocols (low level laser therapy is a promising approach), then every three months would suffice. An ultrasound will need to be ordered by your doctor.

Insurance Coverage/Interpretation: All of the thyroid tests listed above should be covered on insurance, if the practitioner who orders them is an MD, DO, PA or NP. You also have self-order options. I love Ulta Lab because you can self-order the labs, and later submit them to your insurance for reimbursement. (Be sure to check with your individual insurance to make sure they allow this.) This is also a wonderful option for people with a high deductible. While it’s always best to work with a practitioner for an interpretation of these labs (especially if you need a prescription), I’ve also written a comprehensive interpretation guide for your reference.

For a full guide on interpreting your thyroid tests, please see my article: Top 10 Thyroid Tests and How to Interpret Them.

Nutritional Testing

People with Hashimoto’s and thyroid disorders are at a greater risk for nutrient depletions.

Nutritional deficiencies are a two way street. Nutrient deficiencies (especially abnormal ferritin levels) can contribute to thyroid symptoms and can even trigger or exacerbate thyroid disease, while thyroid disorders can lead to nutrient depletions. Thyroid hormones determine our metabolism throughout the entire body. As such, the digestive tract is not spared, particularly the intestines. An insufficient amount of thyroid hormones makes nutrient extraction more difficult and less efficient, and can in itself lead to nutrient deficiencies.

Additionally, most people with thyroid conditions will have low stomach acid (hydrochloric acid, or HCl), which is necessary to break down protein. This can lead to a depletion of amino acids, B vitamins, iron, zinc, and other nutrients obtained from protein.

This is why I recommend testing for a few key nutrients that are vital to thyroid health.

Root Cause Nutrition Panel

The Root Cause Nutrition Panel tests for B12, ferritin, vitamin D, CMP and CBC levels:

• B12 is often lacking in Hashimoto’s, and supplementation is needed because it can result in neuropathy, fatigue or problems with digestion. Optimal B12 levels should be between 700-900 pg/mL.

• Ferritin is an important protein because it stores iron. If you’re deficient in it, then you probably have symptoms like hair loss, fatigue, and poor thyroid function. The optimal ferritin level for thyroid function is between 90-110 ng/mL.

• Vitamin D is a major player in immune system balance. Hashimoto’s patients often have very low vitamin D ranges, and most of my clients who have gotten into remission have optimal levels of this nutrient. Vitamin D levels should be between 60 and 80 ng/L for optimal thyroid receptor and immune system function.

• The CMP (complete metabolic panel) and CBC (complete blood count) will reveal your electrolyte levels, as well as how your cells are doing, how the liver and kidneys are functioning, and whether you are at risk for anemia. The results typically come back “normal” for most people with Hashimoto’s, but it’s important to have these done to rule out serious situations that may require urgent medical interventions.

Insurance Coverage/Interpretation: All of the nutrition tests listed above should be covered on insurance, if the practitioner who orders them is an MD, DO, PA or NP. You also have self-order options. I love Ulta Lab because you can self-order the labs, and later submit them to your insurance for reimbursement. (Be sure to check with your individual insurance to make sure they allow this.) This is also a wonderful option for people with a high deductible. While it’s always best to work with a practitioner for interpretation, I do have protocols for how to address these deficiencies in Hashimoto’s Protocol, as well as a comprehensive article on the most common nutrient deficiencies in those with Hashimoto’s.

Adrenal Testing

In my experience, 9 out of 10 people with Hashimoto’s will be affected by adrenal dysfunction. Treating hypothyroidism without treating the adrenals is one of the biggest reasons people continue to feel exhausted despite receiving treatment with thyroid hormones.

The adrenal glands release hormones such as cortisol and adrenaline. These “stress hormones” impact many important functions throughout the body. They help establish your stress tolerance, tame inflammation, regulate blood sugar and body fat, control potassium and sodium levels (which impact blood sugar), and influence sex drive and anti-aging.

I recommend getting an adrenal saliva test kit (like the Adrenal Stress Profile test by ZRT) for almost everyone with Hashimoto’s. Many symptoms of hypothyroidism actually overlap with poor adrenal function, so it’s important to get an understanding for how well your adrenals are working as you work to address your own root causes. You can read more about addressing adrenal dysfunction here. Along with stress management, I recommend Rootcology Adrenal Support to help restore proper adrenal function.

Insurance Coverage/Interpretation: Generally, adrenal saliva tests are not covered on most insurances because they are considered experimental. Furthermore, most conventional practitioners won’t have access to these tests, as they may not have accounts with the lab. I recommend working with a functional medicine practitioner for interpretation. I also have protocols based on test results in Hashimoto’s Protocol.

Gut Testing

Food Sensitivity Testing

Discovering and removing reactive foods changed my life. I felt incredibly better in just three days after removing dairy. It took me some time before I was willing to commit to this lifestyle change, but if I knew then what I know now, I would have made this diet change a lot sooner!

You can identify food sensitivities by noting your reactions after eating. When we eat foods we’re sensitive to, our body gets exhausted and depleted in energy. Reactive foods trigger an inflammatory response in the GI tract, leading to malabsorption of nutrients, and can also produce intestinal permeability whenever they are eaten.

Sometimes, our body will react to our food sensitivities quickly, and we may experience acid reflux, bloating, irritable bowel syndrome, palpitations, joint pain, anxiety, tingling or headaches.

It’s important to note that food sensitivities cause different types of reactions to foods than food allergies. Food allergies are immediate and often cause life-threatening reactions (picture the child who stops breathing after eating nuts), and are readily acknowledged and tested for by conventional medical doctors, especially allergists. These reactions are known as Type I hypersensitivity reactions and are governed by the IgE branch of the immune system.

However, food sensitivities are considered Type IV delayed hypersensitivity reactions governed by the IgG branch of the immune system—as the name implies, they do not occur right away. In fact, it can take up to four days for them to manifest, and this is one of the reasons why it’s so hard for most people to correlate food sensitivities with symptoms. For example, you may eat corn on Monday and have a panic attack on Wednesday!

Some of the most common symptoms of food sensitivities include post nasal drip, congestion, coughing, asthma, constipation, diarrhea, cramping, bloating, nausea, gas, acid reflux, burning, increased pulse, acne, eczema, itchiness, joint aches, pain, swelling, tingling, numbness, headache, dizziness, brain fog, anxiety, depression, fatigue, and insomnia.

In my experience, whenever we eat foods that flare up our IgG system, this also seems to flare up thyroid antibodies.

Most people will see a dramatic reduction in gut symptoms, brain symptoms, skin breakouts, and pain by eliminating the foods they are sensitive to. Some will also see a significant reduction in thyroid antibodies.

Eliminating a food for a few days (sometimes weeks) will give us a boost in overall health. When we reintroduce a reactive food, we should notice a return of previous symptoms, which will allow us to discern which foods are causing the reactions. This is known as the Elimination Diet.

One of the best ways to identify these delayed food sensitivities is with a blood test that identifies your personal sensitivities to a list of the most common ones. I recommend the 184 Food Allergy IgG test from Alletess or their 96 Food version.

Insurance Coverage/Interpretation: Generally, food sensitivity tests are not covered on most insurances because they are considered experimental, so your best bet is to either work with a practitioner who has access to them or self-order them. While it’s always best to work with a practitioner on interpretation, food sensitivity tests are pretty self explanatory for most people, and most can implement changes based on seeing their own results.

To learn more about testing for and addressing food sensitivities, read my article on food sensitivities and Hashimoto’s.

Testing for Small Intestinal Bacterial Overgrowth

Another possible culprit of your symptoms could be due to Small Intestinal Bacterial Overgrowth (SIBO). Studies have revealed that approximately 54 percent of people with hypothyroidism have SIBO, which can lead to intestinal permeability and contribute to a long list of digestive symptoms including acid reflux, belching, bloating, and irritable bowel syndrome.

Small intestinal overgrowth (SIBO) can be tested with the Small Intestinal Bacterial Overgrowth 3-Hr Lactulose-Genova Kit. Treating SIBO is a crucial component to your healing journey. In some cases, it can put your Hashimoto’s into remission and will help your sugar digestive enzymes regenerate, allowing you to better digest carbohydrates and greatly improve digestive function.

Treatment options vary and can include diets like the low FODMAPs diet, a low-carbohydrate diet, the GAPS diet or the Elemental diet. You can also take herbs like berberine, garlic, and oil of oregano, or even antibiotics like Rifaximin. Furthermore, you can start by removing dairy, as most people with SIBO are lactose intolerant. (You can read more about treatment options here.) Work with your practitioner or functional medical doctor to determine the right course for you.

Insurance Coverage/Interpretation: SIBO has become more accepted by mainstream medicine in recent years. SIBO tests may be covered on most insurances; however, you may have a hard time tracking down a practice that will order them, as not many practitioners are trained in SIBO testing, results and/or treatment. I recommend working with a practitioner to interpret results, and you can visit my article on SIBO for more information on protocols.

Comprehensive Gut Testing

A variety of gut infections and parasites have been implicated in triggering autoimmune thyroiditis, including Helicobacter pylori, Blastocystis hominis, and Yersinia enterocolitica. I’ve found that my clients and readers who do not get better with dietary and nutritional interventions alone, usually have one or more gut infections present exacerbating their condition. Finding and treating these infections often results in a significant reduction in symptoms, and can even lead to remission.

Additionally, most people with Hashimoto’s will have some degree of intestinal dysbiosis (an imbalance in the gut microbiome). Like food sensitivities and SIBO, dysbiosis can cause intestinal permeability and contribute to the autoimmune process and symptoms.

To identify these triggers, I recommend doing a comprehensive stool analysis, like the GI MAP (GI Microbial Assay Plus) – Diagnostic Solutions Kit. This test checks for bacteria, fungi, parasites and viruses in the gut. It also measures bacterial balance of normal flora and digestive markers, like elastase and secretory IgA, which provide further insight on overall digestive and intestinal health.

Insurance Coverage/Interpretation: Comprehensive stool tests may not be covered on insurance plans because they are still considered experimental. However, check with your insurance company, as some may pay for a portion of the test if it is ordered by an MD, DO, PA or NP. Please note, your practitioner has to have an account with each specific company to order the test, and most conventional doctors won’t have access to these types of stool tests. I recommend working with a practitioner to interpret results, and I also have many protocols in Hashimoto’s Protocol based on extensive stool tests.

Organic Acids Test (OAT)

The Organic Acids Test (OAT) by Great Plains Laboratory is a comprehensive urine test that measures markers for vitamin and mineral levels, oxidative stress, neurotransmitter levels, and oxalates. Many people with chronic illnesses excrete abnormal organic acids in their urine. These metabolic byproducts can be measured and can provide insight into hormone and vitamin metabolism, intestinal wall integrity, energy cycle function, neurotransmitter metabolites, and muscle function. I have found that this test can find many more cases of Candida as well as mold, and can also be useful for detecting key nutrient deficiencies such as vitamins B5 and B6, vitamin C, and CoQ10.

Insurance Coverage/Interpretation: Generally, the OAT test is not covered by insurance, so your best bet is to self-order it and work with a practitioner who can order it for you. I recommend working with a practitioner to interpret results.

Infection Testing

Infections are common in those with Hashimoto’s. Sometimes you’ll experience symptoms of the infection, and other times you won’t even know you have it. When I was on my healing journey, I discovered I had four infections! Once I healed them, I noticed a huge difference in my recovery progress.

Potential infections include Lyme disease, Epstein-Barr virus, and Cytomegalovirus. Infections often get the least amount of attention, yet I’ve found that finding an infection and treating it can lead to complete remission in Hashimoto’s.

Did you know? Infections often trigger Hashimoto’s through molecular mimicry. Molecular mimicry is a bit like it sounds. Bacterial or viral cells look a lot like the cells called self-antigens (antigens that originated in our bodies’ cells). In a way, they mimic the good guys. Our immune system gets in “fix it” mode and starts killing off the infection, but in the process, it starts killing off the cells that look a lot like the infection as well. This is a doorway for autoimmunity to usher itself in.

I always recommend my clients test for infections with the Root Cause Infections Panel because treating infections can alleviate a lot of symptoms, and can sometimes put Hashimoto’s into remission by identifying and then healing them. Treatment options vary between antibiotics and herbal protocols, or a mixture of both, as I note in my book Hashimoto’s Protocol. Your doctor can help you decide which is best. Read more about addressing infections here.

Insurance/Interpretation: All of the infection tests listed above should be covered on insurance, if the practitioner who orders them is an MD, DO, PA or NP. You also have self-order options. I love Ulta Lab because you can self-order the labs, and later submit them to your insurance for reimbursement. (Be sure to check with your individual insurance to make sure they allow this.) This is also a wonderful option for people with a high deductible. I recommend working with a practitioner to interpret results.

Genetic Testing

A variation to the MTHFR (Methylenetetrahydrofolate Reductase) gene is incredibly common. In fact, it’s present in up to 55 percent of the European population, is naturally occurring, and often has no negative health consequences—unless expressed.

The gene codes for the MTHFR enzyme, the enzyme that converts the amino acid homocysteine to methionine, a building block for proteins. As a result, individuals with a genetic variation and low activity of the MTHFR enzyme may present with elevated homocysteine levels, which have been associated with inflammation, heart disease, pregnancy complications, and even miscarriages. This has also been associated with higher rates of Down syndrome and birth defects in offspring, as well as other issues such as depression, an increased risk of blood clots, and a higher risk of certain cancers. Some of my clients with Hashimoto’s and the MTHFR gene variation have even reported having bigger blood clots during their menstrual cycles.

One of the key things to note is that this gene variation also prevents people from properly methylating, which is one of the body’s key detox processes that helps them get rid of toxins. Methylation impairment can result in an impaired ability to clear out certain toxins such as mercury and arsenic; and may lead to estrogen dominance. Symptoms like brain fog, multiple chemical sensitivities, depression, irritability and anxiety are related to impaired methylation, and as they are all too common symptoms in Hashimoto’s, I designed the MTHFR Pathways supplement by Rootcology to help support the methylation pathways.

Insurance/Interpretation: The MTHFR gene can be identified through a DNA analysis test, such as the one from Ulta Labs. I love Ulta Lab because you can self-order the labs, and later submit them to your insurance for reimbursement. (Be sure to check with your individual insurance to make sure they allow this.) This is also a wonderful option for people with a high deductible. You can also order a saliva test kit from 23andme.com, and upload your results to geneticgenie.org, which will then tell you if you have the genetic variation.

Next Steps

I hope these tests help you on your healing journey. I highly recommend working with a Functional Medicine doctor as you navigate testing, and I’ve put together a list of doctors to help you find someone in your own area. Download my free guides below!

If, for whatever reason, you are unable to get a doctor to order the tests for you, you always have the option of self-ordering the recommended tests online.

Testing can be costly, but it’s an important piece to your remission puzzle. I gave up shopping during my process to pay for certain tests. That was a big deal for me since shopping helped me cope with feeling so awful all the time. In the end, getting my Hashimoto’s into remission made the trade off so worth it! I hope ordering tests will help you uncover your root causes and feel better as well.

P.S. You can also download a free Thyroid Diet Guide, 10 thyroid friendly recipes, and the Nutrient Depletions and Digestion chapter of my Root Cause book for free by signing up for my weekly newsletter. You will also receive occasional updates about new research, resources, giveaways, and helpful information.