Hashimoto’s Thyroiditis Part 1: Testing and Diagnosis

Although Hashimoto’s thyroiditis may sound like something you’d get at a sushi bar, the term applies to a type of inflammation found in the thyroid gland (a gland located over the front of the throat). 

The type of inflammation is not usually due to an infection, but to the body’s immune system mistakenly tagging thyroid cells as “bad”.  This is why Hashimoto’s is considered an auto-immune disease, since a normal immune response is to tag potential invaders like bacteria (not the body’s own cells).  As a result, the thyroid slowly gets destroyed over time.

For reasons still unknown to us, Hashimoto’s mainly affects women.  Some theories include:

  • Higher estrogen (from birth control pills, post-pregnancy, estrogen-dominance, etc)
  • Personal care products: Women tend to apply more products to their hair/skin that disrupt hormones (e.g. xenoestrogens).
  • Body fat: Women have a higher body fat percentage than men. One reason this makes a difference is that many chemicals we encounter tend to accumulate in fat cells due to their “fat-preferred” nature (aka “lipophilic”)
  • Internalized stress: Women are more likely to have circadian rhythm imbalances from the pressures of work/home life, disrupted sleep, cortisol-driven inflammation, lack of self-care, etc.

I personally have this condition, and I know what it feels like to only be provided a few options for treatment, namely prescriptions, surgery, or do nothing.  And these options work for a lot of people!  But when these don’t work, many patients with the symptoms of Hashimoto’s (whether diagnosed or not) are handed anti-depressants, told that they are “just stressed”, are advised to lose weight by “eating less and exercising more”, or are told that their labs are normal so there’s nothing more to do.

This is where functional medicine steps in (although I think it should be used first, to avoid dealing with the above frustrations!). 

This is Part 1 of a series of articles I’m putting together.  I’m going to focus on my personal approach to Hashimoto’s, which is a combination of functional medicine and immunology, and give as many tips for self-care as possible.

  • Part 1 (current article): Diagnosis (including symptoms and lab testing)
  • Part 2: Causes of Hashimoto’s
  • Part 3: Treatments (including pharmaceutical, supplements, and alternative approaches)

Of note, Hashimoto’s is not a thyroid problem – it is a problem with the immune system.  You can have this managed with just thyroid hormone replacement, but it is important to address the balance of the immune system to prevent future autoimmune conditions (since 25% or more of those with one autoimmune condition are at risk of developing another).  It comes down to having the “perfect cascade” of triggers, which I will discuss in Part 2.

Autoimmune diseases like Hashimoto’s often go undiagnosed for years.  Why?

  • Symptoms of Hashimoto’s often seem unrelated, and may not follow the typical patterns seen in hypothyroidism or hyperthyroidism.  For example, my symptoms presented with extreme muscle fatigue, palpitations, and “brain fog”.  I didn’t have changes in my skin, weight, sleep, or bowel movements.  See below for a list of some of the more common symptoms.
  • It is not in the mainstream lab “algorithm” to look for antibodies that diagnose Hashimoto’s.  Although the latest endocrine guidelines suggest this should be done, most doctors and healthcare practitioners do not check more than a TSH. 
  • In mainstream medicine, our medical education taught us that looking for autoimmune conditions didn’t provide a lot of addition information that we could do something about. There are drugs that work for various autoimmune conditions, but there aren’t any drugs that specifically address the autoimmunity associated with Hashimoto’s.  Thus, most Hashimoto’s patients are only able to be treated with thyroid hormone replacement medication. 



There are potentially 300+ symptoms that are associated with Hashimoto’s.  The following is an overview of common symptoms I’ve seen, but there is never a “typical” presentation:

  • Weight problems (gaining or losing weight)
  • Fatigue
  • Insomnia
  • Mood imbalances (anxiety, depression, mood swings)
  • “Brain fog”
  • Digestive issues like bloating and “IBS”
  • Palpitations
  • High cholesterol
  • Body aches, muscle weakness (often diagnosed as fibromyalgia)
  • Hormonal imbalances (low libido, irregular periods, miscarriages, infertility)
  • Migraines


If your doctor or healthcare practitioner suspects your symptoms are related to your thyroid, they will often start with ordering a TSH (Thyroid Stimulating Hormone) test.  Sometimes, they may also order a free T4, but many medical organizations advise only to do this if the TSH is out of the lab’s reference range. 

Although the above is great for SCREENING and overt DIAGNOSIS of hypo- or hyperthyroidism, it is not great at looking at patterns that indicate biological dysfunction, and it will not diagnose Hashimoto’s.  There are some limitations with the above approach, if looking for Hashimoto’s or even subclinical hypothyroidism.

  • It is a limited test panel. 
  • A lab’s reference range is not the best range to go off of (see here for more on how labs determine these ranges)
  • There is no evaluation of lifestyle habits (these trigger most imbalances)
  • There is no imaging testing (i.e. ultrasound)
  • Antibodies are not evaluated.

Quick tangent, on cost for labs.  Having worked in both mainstream medicine and functional medicine, I have learned that there are a lot of tests that would be great to run on everyone, but insurance is picky on what they will or will not cover.  What they don’t cover, the patient has to pay (and I’ve seen patients billed up to $800 for just the full thyroid panel!).  This is part of the reason that many mainstream practitioners will not run more tests, since they are contracted with insurance companies and insurance will break a contract if the practitioner goes against insurance “rules”.  And although most of my functional medicine colleagues rely on testing, we really don’t have to do so much excessive testing (in my personal opinion and experience).

By the way, all my patients use insurance to cover labs in my practice.  If they don’t have insurance, we have labs that offer cash prices (which are usually ⅓- the cost billed to insurance). 


There are only two labs that can truly confirm Hashimoto’s thyroiditis, which is the presence of high TPO or Tg antibodies.  What many don’t know, though, is that these usually have to be in the hundreds before we see destruction of the thyroid gland.  Thus, if the normal TPO antibody level is under 9, and a result is 90, this may indicate the potential for thyroid autoimmunity but unlikely to have full-blown Hashimoto’s (or Grave’s Disease, since this marker can also be high in Grave’s) .  Lower levels only indicate immune activation. 

To confirm thyroid destruction, regardless of the lab value for antibodies, a thyroid ultrasound is needed (with a report on “echogenicity”).

If someone presents with symptoms that suggest Hashimoto’s, I like to order a comprehensive lab panel before “functional” tests (since most functional tests are not covered by insurance, but the following lab panel is more likely to be covered).  Most of these can be ordered through a mainstream practitioner (if willing and able!). 


What labs do I recommend?

  • Full thyroid panel (TSH, free T3, free T4, TPO antibodies; +/-  reverse T3, Tg antibodies).  See video I did on these here.
    • TSH: This isn’t made by the thyroid, but it is a hormone made by the brain that acts like a “text message” to the thyroid (to tell the thyroid to make more hormones).  More messages will be sent to the thyroid if the brain feels like the thyroid isn’t making enough thyroid hormones (T4 and T3).
    • Free T4: The primary hormone made by the thyroid.  This actually is a “pro-hormone”, meaning it’s main purpose is to turn into the active thyroid hormone (T3) or the inactive thyroid hormone (reverse T3).  I call this the “Clark Kent” hormone.
    • Free T3: The hormone that does all the work, aka the active thyroid hormone (or “Superman”).  The thyroid does make some of this, but most of this is made via “thyroid conversion” (turning T4 into T3).  This is mostly done in the liver, gut, and metabolically active tissues (thus, if these organs aren’t working well, we can experience hypothyroid symptoms!).
    • TPO antibodies: These usually become present up to 10 years before we see changes in thyroid hormone levels.  Over 90% of people with Hashimoto’s will have high TPO antibodies.  Contrary to popular belief, high antibodies does NOT directly equate to more thyroid destruction – it simply indicates an immune system that is reacting to a trigger.
    • Reverse T3 (optional): T4 has the option to turn into reverse T3 or active T3, and normally 20% of this hormone will turn into reverse T3.  Reverse T3 is analogous to an irreversible “brake” (and active T3 is the “gas pedal”).  When reverse T3 is higher, it can block active T3 from doing it’s job (since these compete for the same pathways).  This is often touted by my functional medicine colleagues as one of the essential hormones to evaluate, but since it can be expensive (it is considered “experimental” by most insurance companies), I find it doesn’t affect my treatment approach as much.  Typically, a high reverse T3 does not tell me the cause (and I check the most common causes already).  I will check this, but usually on the second or third follow up thyroid test.
    • Thyroglobulin (Tg) antibodies (optional): Just like TPO antibodies, these will increase up to 10 years before thyroid hormone levels are affected.  But it’s not as specific to Hashimoto’s (meaning around 50% of those with Hashimoto’s will have high Tg antibodies).
  • Complete Blood Count (CBC): This is a very inexpensive test, which most insurance companies will cover.  It typically looks for overt problems like anemia, cancers, and infections. I look at the nuanced patterns in this, most of which are not flagged as “abnormal”, which tell me how the immune system is actually working.
  • Complete Metabolic Panel (CMP): This is also very inexpensive, and looks for problems with the kidney and liver.  I also use this to look for optimal levels of electrolytes and liver enzymes (remember, a lot of the active thyroid hormone is made in the liver!).
  • Basic Lipid (cholesterol) Panel: Did you know that this was the first test used to diagnose hypothyroidism, before we could test for thyroid hormones?  I still use it to look for potential issues with the liver, blood sugar, inflammation, and cardiovascular function.
  • Vitamin D3 (25-OH): This is involved in immunity, and I’ve had a handful of patients feel better just by optimizing this value (which can take 3-6 months to improve, with the right dose). 
  • Homocysteine: This is an inflammatory marker, but I use it to determine if a patient needs more of certain B vitamins (many of which impact hormone balance and energy).  
  • Ferritin: This is a protein that looks at iron reserve.  Iron is needed for delivering oxygen to cells/tissues around the body, and it is involved in thyroid hormone production.  Many of the symptoms of low iron and hypothyroidism are similar.  
  • Insulin: I call this the “fat fertilizer” hormone.  If this is too high, many patients will have hypothyroid symptoms (for example, higher levels indicate a road towards insulin resistance and increased inflammation). 
  • Cortisol: This is a hormone that regulates how our body responds to stress, and is supposed to give us more energy (by releasing glucose into our blood – not great for diabetics!) or act as an anti-inflammatory (steroids are related to cortisol).  However, it will also do the opposite actions if chronically dysregulated.  Checking this in the blood should mainly be as a screening tool, and I won’t use this to determine treatments.  I will often use a saliva-based test to truly determine how someone’s cortisol patterns are affecting their health (the test I use is under $100) and to determine treatment.
  • Celiac Disease panel (4 tests).  Since most people with Celiac Disease do not have gut symptoms, I will run this if someone is still consuming gluten (not useful if someone is already gluten-free).  The symptoms of Celiac Disease are often similar to those seen in thyroid conditions.

The above is all found on a blood test, and evaluating the results depends on the background of the practitioner.  More than half of these will look “normal” on a lab, due to the lab’s pre-determined reference ranges.



There is some variation in opinion about what constitutes a “normal” or “optimal” lab value, even in functional medicine  For example, my functional medicine training recommends a TSH value between 0.5 and 2.5, but I’ve encountered practitioners that prefer to keep TSH levels around 1-1.5.  Like anything in medicine, there is no one-size-fits-all and I advise caution to both patients and practitioners if treatment is based on lab values rather than symptom improvement.  Labs are only guides, and there are a lot of factors that can affect lab results.  A few examples:

  • Many patients will experience palpitations (feeling like the heart is racing) or anxiety if on the wrong dose of medication.  I’ve had over a dozen patients get evaluated by a cardiologist, only to find out that the thyroid medication was causing the problem.  Many of these patients felt better with a TSH around 2.5, and free T3 just under the “optimal” range (optimal range is around 3.2 to 3.6).
  • I personally cannot tolerate an “optimal” free T3 level, and my free T3 runs around 2.8-3.0. 
  • Too often I have had a patient be hyper-focused on improving a lab result by something as little as 0.2 (which was instructed to them by online blog articles, books, forums, or even a practitioner’s guide), but thyroid hormone levels fluctuate, often down to the hour at which thyroid hormones are tested! 

I’m not saying that we shouldn’t use optimal lab ranges as a target for treatment, but I do advise that both patients and practitioners don’t get caught up in treating the labs!  Thyroid hormone imbalances are only a part of what drives symptoms (remember where these are converted – see above).

Based on the patterns of the results above, our next step is to determine what is causing immune activation while improving symptoms.  This may involve additional testing such as stool or urine-based testing (i.e. “functional tests”), and often requires 4+ appointments over the course of a few months.



  • Hashimoto’s thyroiditis is an autoimmune condition that involves the thyroid gland.
  • It is a problem with the immune system.
  • Most that have Hashimoto’s will experience both hyperthyroid and hypothyroid symptoms.
  • Hashimoto’s is significantly under-diagnosed.
  • The best tests to diagnose Hashimoto’s are: high TPO antibodies, high Tg antibodies, and/or changes seen on a thyroid ultrasound.
  • Mainstream medicine often misses Hashimoto’s diagnosis because of limited testing, and limited ability to treat high antibodies.
  • A lot of information can be obtained from a simple blood test, with the right tests!

If you are interested in working with me, I’d love to help!  Starting in January 2021, I’m joining the amazing team at Parsley Health!  Click here if you want to join me!

The information contained in this article is for educational purposes only.  It does not constitute a diagnosis or prescription for treatment.



  1. Article on xenoestrogens in skincare: https://lauraschoenfeldrd.com/xenoestrogens-in-skincare/
  2. 2001 study on lipophilic toxins: https://www.ncbi.nlm.nih.gov/pubmed/11834080
  3. 2010 study on increased risk for additional autoimmune conditions in those with thyroid autoimmunity: https://www.thyroid.org/patient-thyroid-information/ct-for-patients/vol-3-issue-4/vol-3-issue-4-p-7-8/
  4. 2010 study on increased risk for multiple autoimmune conditions (in general): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150011/
  5. Latest (2015) Guidelines from the 2 main American endocrine societies (ATA/AACE): http://content.guidelinecentral.com/guideline/get/pdf/3295 
  6. List of 300 symptoms associated with hypothyroidism: https://hypothyroidmom.com/300-hypothyroidism-symptoms-count-how-many-you-have/
  7. The trouble with reference ranges: https://academic.oup.com/ajcp/article/133/2/180/1760481
  8. Use of ultrasound in evaluating autoimmune thyroid conditions: https://www.ncbi.nlm.nih.gov/pubmed/10779140
  9. Conversion of T4 to T3: https://drknews.com/conversion-t4-t3-important-consideration-low-thyroid-function/
  10. Antibodies in thyroid disease: https://www.thyroid.org/patient-thyroid-information/ct-for-patients/vol-7-issue-9/vol-7-issue-9-p-10-11/
  11. Vitamin D and the Immune System: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166406/
  12. Insulin resistance and thyroid dysfunction: https://www.endocrine-abstracts.org/ea/0041/ea0041ep1055
  13. Article (2003) that lists common symptoms caused by gluten: https://academic.oup.com/brain/article/126/3/685/321208?fbclid=IwAR0gBLri8dTaQQ485zBLLgbNHvYBy6sF1judpuvOvYbU11GYki_PR5FQqYs