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Why Your Thyroid Diagnosis Might Be a Misdiagnosis

Thyroid Symptoms Like Brain Fog and Fatigue May Actually Be Coming From Your Gut

Key Takeaways:
  • An underactive thyroid diagnosis can cover anything from the autoimmune disorder Hashimoto’s thyroiditis, through subclinical hypothyroidism and clinical hypothyroidism without autoimmunity.
  • Hypothyroid conditions are often diagnosed and medicated too early.
  • In many cases, a wait-and-see approach is more appropriate as thyroid hormone levels can correct themselves without medication.
  • Gut health and thyroid health are closely related; sometimes symptoms that seem like thyroid symptoms might actually be due to gut issues.
  • Improving your gut health with a healthy diet, probiotics, and limiting foods you might be intolerant or sensitive to may improve your thyroid gland function.
  • Gut therapy may even mean you don’t need to use thyroid hormones or can reduce the dosage.

Were you given an underactive thyroid diagnosis, or are you experiencing symptoms that you suspect are from low levels of thyroid hormones? If so, you’re not alone. In fact, around one in twenty Americans have some degree of hypothyroidism [1]. Symptoms, when you get them, can include fatigue and brain fog, dry skin, weight gain, and feeling cold.

When hypothyroidism is a clear clinical diagnosis, treatment with thyroid hormones can be a life-changer. You can expect your energy levels to lift, your mood to improve, and your thoughts to be clearer. 

However, in this article, I want to cover the less clear-cut cases of hypothyroid diagnosis, which we see many of in the clinic. 

For example, you may have started taking thyroid hormones based on lab test results, not symptoms. Or maybe you can’t get the dose right or are still having symptoms despite your hormone levels returning to normal. 

The reality is that there are a lot of well-meaning but off-target treatments out there for thyroid disorders. 



More specifically, within the functional medicine space, there’s a tendency to overdiagnose and overtreat hypothyroidism. This laser focus on “treating the numbers” can be a distraction from investigating other potential problems, like gut imbalances,  which may actually underlie hypothyroid symptoms.

These issues make diagnosing hypothyroidism a lot more complicated than it needs to be, which has created a lot of confusion for both patients and providers. But the good news is that hypothyroidism is frequently easier to diagnose than most think, as I’ll explain below.

Let’s dig into your underactive thyroid diagnosis to find out what may actually be going on under the surface. Before getting started, it’s helpful to clarify some of the terminology around hypothyroidism.

Defining Hypothyroid

You’re probably familiar with terms such as hypothyroid, sluggish thyroid, and underactive thyroid. Though these all roughly describe the situation that your thyroid likely isn’t working as well as it should, it’s helpful to understand the descriptions around hypothyroidism a little better.

This way, you and your healthcare provider will be working from the same page, and you’ll also be able to understand when the terminology is a little off.

Here’s a quick explainer:

Clinical Hypothyroidism 

Clinical hypothyroidism (also known as overt hypothyroidism, frank hypothyroidism, or just hypothyroidism) is a clear-cut diagnosis when a blood test shows that you have:

  • Low levels of the thyroid hormone thyroxine (T4) released by the thyroid gland (free T4 below 0.82 mg/dL) [2].
  • AND high levels of thyroid stimulating hormone (TSH), released by the pituitary gland (above 4.5 IU/mL) [3]. 

The correct course of action for clinical hypothyroidism is to treat with thyroid hormone, usually the medication levothyroxine.

Subclinical Hypothyroidism 

Subclinical hypothyroidism is when levels of thyroxine T4 hormone are normal, but levels of TSH are high. 

However, in some situations, like being in an older age group, it’s perfectly normal for TSH levels to be somewhat above the “normal” range without any symptoms.

It may not be accurate to label everyone with marginally high TSH levels as having medicable hypothyroidism.

In any case, mild symptoms of subclinical hypothyroidism can often be treated with appropriate diet and lifestyle steps, and may not need hormone therapy.

Hashimoto’s Disease or Hashimoto’s Thyroiditis 

Hashiomoto’s is the autoimmune disorder that is the most common cause of subclinical and hypothyroidism in the USA (in some other parts of the world low iodine consumption is a more common cause) [1]. 

It may or may not present with hypothyroid symptoms (depending on your TSH and T4 levels), but if you have a Hashimoto’s diagnosis, you’ll want to monitor your labs and any symptoms to see if they progress. 

A sign of having Hashimoto’s is if your levels of thyroid peroxidase (TPO) antibodies are high. Research suggests the presence of these antibodies is 90% sensitive in detecting thyroiditis [4].

It’s important to note that having Hashimoto’s doesn’t mean you will definitely go on to develop full-blown hypothyroidism, though it’s more likely if you have very high TPO antibodies above 500 IU/mL [5].

In fact, the Tehran Thyroid Study, which followed the course of thyroid disease in a large cohort of people over nine years, found those with elevated TPO antibodies (indicative of Hashiomoto’s) only had a 9–19% chance of becoming hypothyroid after 6 years of follow up [6, 7]. 

TG (thyroglobulin) antibodies may also be included in antibody testing, but they do not accurately predict autoimmunity [8].

One of the most effective ways to help autoimmune conditions (and thereby prevent Hashimoto’s progressing into hypothyroidism) is to improve your gut health. I’ll develop this idea in more detail below.

Underactive or Sluggish Thyroid

These two terms don’t have any specific medical meaning. They can encompass anything on the hypothyroid spectrum — from subclinical hypothyroidism with no symptoms, to being symptomatic with non-specific symptoms (fatigue, constipation, hair loss, etc.) but with all thyroid labs within normal limits.

Many well-intentioned functional medicine providers will often prescribe thyroid medication to people who fall along this spectrum. However, I frequently see that “sluggish thyroid” patients won’t respond to thyroid hormone — instead, a gut–healing protocol often leads to greater symptom improvement. 

Thyroid Conditions are Over-Diagnosed and Over-Medicated

Both conventional and natural medicine practitioners are prone to over-diagnosing hypothyroidism. 

If it feels like your doctor rushed to diagnose you and get you started on medication, I’d advise that you get a second opinion.

More specifically, if the labs used to diagnose you did NOT show abnormally high TSH paired with abnormally low T4, then you likely are not clinically hypothyroid and may not need medication. 

One interesting study involved a group of nearly 300 patients who had been taking thyroid hormone replacement therapy for years, despite not having strong diagnostic indicators of hypothyroidism. 

During the trial, these patients stopped taking their thyroid hormone medication (levothyroxine) for 6–8 weeks while being monitored by researchers [9]. After going without thyroid hormone replacement for several weeks:

  • 61% of patients returned normal thyroid function test results 
  • These patients were able to stay off their thyroid medication longer term 

Another study validated these findings and showed that subclinical hypothyroidism will often correct itself without any intervention. The study followed 225 people diagnosed with subclinical hypothyroidism through a population screening program. This group was followed for 6 months with no treatment. After this time, the vast majority (73.8%) had moved back out of the hypothyroid range and had normal TSH levels again [10]. 

This suggests hypothyroidism can be transient, and a watch-and-see is often best. There is no need to rush to hormone treatment unless you fall into the overt hypothyroidism category.

That said, your thyroid could always use some attention, especially if you are having symptoms. In my experience, the best way to look after your thyroid and stave off hypothyroidism is to address gut health problems. 

Gut Health is Key to Thyroid Health

Some patients with subclinical hypothyroidism find their TSH levels and symptoms normalize once issues with their gut health (such as gut infections, leaky gut, and microbiome imbalances) have been addressed. As a result, people can sometimes prevent having to take thyroid medication or can come off medication they were already prescribed. 

Other patients will need to continue with thyroid hormone replacement therapy. However, I’ve seen several cases where, after a gut-healing program, the patient’s digestive system absorbs the hormone medication better and the patient can reduce their dose. 

Why does poor gut health impact the thyroid gland so much? Well, when our gut microbiome is imbalanced, it can create inflammation and immune system abnormalities that also affect thyroid function and thyroid hormone production. More specifically, [11, 12]:

  • Altered immune responses in the gut can contribute to or aggravate autoimmune conditions, including Hashimoto’s thyroiditis.
  • Poor gut health can alter the activity of enzymes that impact thyroid hormone levels and reduce the absorption of minerals important to thyroid health.
  • Gut inflammation can trigger brain fog, depression, and other cognitive issues that are similar to hypothyroid symptoms. 

Thyroid Symptoms or Gut Symptoms?

The final bullet point above is important because thyroid symptoms can sometimes be confused with gut symptoms. This can explain why some patients who have received treatment for a hypothyroid diagnosis continue to have symptoms despite now having entirely normal thyroid hormone levels. 

In fact, we saw so many patients in the clinic for whom this was the case, that we published a case series and literature review to alert other functional and integrative practitioners to this observation.

Symptoms that can masquerade as thyroid problems, but are actually gut-related include fatigue, anxiety, brain fog, and depression [13, 14, 15, 16, 17, 18].

These residual problems won’t go away with continued hypothyroid treatment because it is not the thyroid that is at issue, but the gut.

Diet and Probiotics Are Key Strategies in Gut Healing

To improve your gut health in a way that will underpin good thyroid health, a diet that is anti-inflammatory, nutrient-rich, and takes account of foods you may be intolerant or sensitive to is a good base.

Finding a Diet that Fits

Many of my patients do well using a Paleo diet framework, as it checks the above boxes without being overly restrictive.

A Paleo diet usually minimizes gluten and lactose, which research suggests are two of the commonest food sensitivities in people with hypothyroid issues.

For example, two studies showed lactose restriction and a gluten-free diet were associated with significant decreases in TSH levels for Hashimoto’s patients on thyroid medication [19, 20]. That said, you should monitor your reactions using a food and symptoms diary. If you seem to tolerate wheat and dairy well, i.e. you don’t react with gas, bloating, abdominal cramps, or other symptoms after you eat them, there’s no need to remove them.

Some people find their thyroid and gut symptoms worsen when they eat too many of certain carbohydrates known as FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols). This can feel counterintuitive if you are affected because FODMAPs are found mainly in healthy high-fiber plant foods like garlic, onions, apples, and mangos, for example. The reason FODMAPs are an issue if you have a particularly sensitive gut, is that gut bacteria like to ferment them, producing a lot of gas.

If your tolerance to a healthy plant-based, high-fiber diet seems low, particularly if you have pre-existing irritable bowel syndrome, a low FODMAP diet may best suit your needs [21].

As your gut heals, you’ll be able to tolerate more foods and get back to a more varied diet, which is ultimately good for your gut microbiome health. You can find much more detail about elimination diets and how to do them safely for thyroid conditions if you sign up for my Thyroid Self Help Guide.

Probiotics Can Be a Game-Changer 

Probiotics can be super helpful in getting your gut back in shape. Here are some of the ways that they can promote better gut health.

  • Increase the bacterial diversity, or health, of your bacterial community [22, 23, 24]
  • Fight pathogens (harmful bugs) and their toxins [22, 23, 25, 26, 27)
  • Promote a more rapid recovery from imbalanced gut organisms [22, 23]
  • Promote a healthy immune response in your gut [22, 23, 28, 29, 30]
  • Reduce gut inflammation [22, 23, 24]
  • Encourage the growth of healthier microbes in your gut [22, 23, 28]
  • Reduce leaky gut, which is damage to your gut lining [22, 23, 31, 32, 33]

Remember, probiotics create a healthy gut, which means a healthier thyroid. One study found that when thyroid patients improved their gut health by using probiotics, they were able to use less of the thyroid medication levothyroxine (Synthroid) [34]

If you’re a little confused about which probiotics to take, it helps to know that nearly every probiotic product can be classified into one of these three categories [35].

  • Lactobacillus and Bifidobacterium
  • Saccharomyces boulardii (a healthy fungus)
  • Soil-based bacillus species

Some patients do well with taking just one product from one category — usually a Lactobacillus and Bifidobacterium blend. However, studies suggest mixtures of probiotics taken together tend to be more effective [36, 37]. The feedback we get from patients at the clinic suggests that a triple therapy approach, which means taking one probiotic from each of these three categories, often achieves better results. 

Regardless, it’s fair to give probiotics a trial period of 2–3 months to make sure you give your body a chance to reap the full benefits. 

Other Supplements That Might Help

Probiotics are the only supplement that I would routinely recommend for everyone with thyroid disease. But there are some other supplements that I want to draw your attention to that might be of use depending on your individual circumstances. This table breaks down these and gives you an idea of if or when you might benefit

Vitamin D

Thyroid Health Connection Practical Advice
  • Low vitamin D levels are associated with hypothyroidism [38, 39]. 
  • Research suggests that vitamin D supplements can improve autoimmune hypothyroidism measured through a reduction in TPO antibodies [40, 41, 42, 43]
Overall, vitamin D is worth taking, as deficiency is common, especially if you have cold, dark winters or get minimal sun exposure. You can have your levels tested easily and inexpensively if you want a definitive answer about your vitamin D status. Take Vitamin D for at least 3 months to see if there is a notable effect on hypothyroid symptoms [42]. 

Selenium

Thyroid Health Connection Practical Advice
  • Selenium can improve thyroid antibodies, postpartum Hashimoto’s, and thyroid gland structure as measured by an ultrasound thyroid scan (an imaging test) [44] [45].
  • Hypothyroidism patients also tend to have lower thyroid antibodies than those who didn’t take selenium [46].
Not all studies show the benefits of selenium in helping a thyroid diagnosis [47, 48]. There appears to be no downside though, and because selenium is neither expensive nor invasive, it seems reasonable to try selenium supplements and see how you respond. 

Betaine Hydrochloride (HCL)

Thyroid Health Connection Practical Advice
  • Research shows that up to 40% of hypothyroid patients also have stomach autoimmunity, resulting in low stomach acid [49, 50]. Betaine HCl is a supplement that can increase stomach acid levels.
Reasons to consider betaine HCL for hypothyroid issues are if you have a history of autoimmune diseases (other than Hashiomoto’s) are over 65, or have a history of anemia.

Iron

Thyroid Health Connection Practical Advice
  • A small study showed that low iron (measured as serum ferritin) was correlated with lab markers for hypothyroidism [51]. 
  • Another study showed that iron deficiency was related to thyroid hormone status [52]. 
It’s best to be tested for low iron stores before supplementing, as too much iron can increase oxidation in the body [53]. Being a woman with heavy periods, and eating only a plant-based diet are risk factors for iron deficiency. 

Zinc

Thyroid Health Connection Practical Advice
  • A systematic review found a correlation between the severity of hypothyroidism and low zinc and selenium levels [54]. 
  • In a clinical trial, 6 months of zinc supplementation improved serum thyroid markers [55]
The data on zinc and hypothyroid isn’t definitive. Therefore, supplemental zinc may be worth a 1-month trial, and if no improvements, discontinue.

What About Iodine?

Though iodine deficiency is a key cause of hypothyroidism (goiter) in some parts of the world, too much can also be a problem. Supplementation is not recommended in the USA, where iodine intakes are generally sufficient. That’s because too much iodine can actually increase the incidence of thyroid autoimmunity [56] and is a risk factor for hypothyroidism [57].

This means you should only take supplemental iodine if you know you’re definitely deficient.

If You Need Medication, You Need Medication

Though I’ve made the case that many patients are given thyroid hormone replacement therapy too readily, medication can be important. If your T4 and TSH tests indicate it is necessary (see above in the Defining Hypothyroid section), you should definitely go ahead with it.

The conventional medicine choice is usually to give the T4 thyroxine hormone in its synthetic form (levothyroxine).

However, there is another, more active, thyroid hormone known as triiodothyronine or T3 used in the body. We naturally make it by converting T4 to T3 in the body, but T3 can also be taken as a medication.

Many functional health practitioners prefer using a combination of T4 and T3 (from desiccated pig thyroid). They do this on the basis that the body might have a hard time converting T4 to T3. 

However, the evidence for combination T3 and T4 therapy isn’t impressive. One meta-analysis (the highest quality type of research) and a review have shown that there is no reliable evidence that combination T4 and T3 is better than T4 monotherapy for treating symptoms [58, 59]. 

That said, a review paper found that patients preferred T3/T4 combination therapy over T4 alone 50–70% of the time [59].

Overall, I prefer to use synthetic T4 as we know it works and is a more consistent and regulated product without significant side effects. The American Thyroid Association also does not recommend combining T4 and T3 [60].

If T4 monotherapy doesn’t resolve my patient’s symptoms, or if they feel unhappy with their results, then I’ll consider moving on to a combination of T3 and T4.


Thyroid Diagnosis: It’s Nuanced

If you’ve been uncertain or confused about your hypothyroid symptoms or thyroid hormone levels, I hope you now understand more of the complexity around this topic. 

The bottom line is that hypothyroidism is a wide spectrum and, depending where you are on that spectrum, you may or may not need hormone therapy.

Whether you require medication or not, it pays to look after your underlying gut health, which can help reduce symptoms such as brain fog and fatigue that are typical of both gut problems and hypothyroidism.

If you’d like to work through your thyroid issues in more depth, you should check out my thyroid course, which will show you how to self-manage thyroid conditions. Or, if you prefer, reach out for a virtual one-to-one consultation with one of our highly experienced practitioners.

The Ruscio Institute has also developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

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