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The Often Overlooked Gut-Thyroid Connection

Your thyroid symptoms could be coming from your gut.

If you’ve been diagnosed with a thyroid condition, like Hashimoto’s disease, you may assume that your symptoms of fatigue, brain fog, poor mood, and constipation are the result of poor thyroid function.

However, if you are taking thyroid medication and your TSH and free T4 levels are normal, it’s unlikely that you are experiencing thyroid symptoms. Poor gut health is a more likely cause. The connection between gut health and thyroid health is backed by a significant amount of research, yet it’s often overlooked in clinical practice.

The Often Overlooked Gut-Thyroid Connection - Thyroid%20Medication 16%20x%209 Landscape L

Scientific evidence shows a strong connection between thyroid health and gut health. Based on current research, we know that:

  • Thyroid conditions and gut conditions tend to occur together [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
  • Fatigue, depression, anxiety, brain fog, and headache are common symptoms of gut conditions [4, 13, 14, 15, 16, 17, 18]
  • Treating gut conditions can improve thyroid health  [7, 8, 19, 20, 21, 22, 23, 24

Good thyroid health starts in the gut. Simple, gut-directed therapies can help you to resolve frustrating symptoms, reduce thyroid inflammation, reduce thyroid antibodies, and, in some cases, reduce thyroid medication.

In this article we’ll explore the scientific facts behind the gut-thyroid connection and provide helpful tips to get you on the road to better gut and thyroid health.

Gut and Thyroid Conditions Are Linked

Even if you don’t have obvious gut symptoms, it’s important to know that gut conditions and thyroid conditions are very often found in the same patients. Here are some examples from the research:

Celiac Disease and Non-Celiac Gluten Sensitivity
  • Multiple studies have found that autoimmune thyroid disease is more common in patients with celiac disease [1, 2] and non-celiac gluten sensitivity [3, 4
Leaky Gut
  • Children with Hashimoto’s disease were found to have more markers of leaky gut when compared to controls [5]
Low Stomach Acid
  • Up to 40% of Hashimoto’s patients were found to have chronic low stomach acid [6]
  • Thyroid patients with low stomach acid require higher doses of Levothyroxine (Synthroid) [7, 8]
Small Intestinal Bacterial Overgrowth
  • SIBO patients were more likely to have impaired thyroid function than healthy controls [9]
  • In a study of SIBO patients, the two most common co-existing health conditions were hypothyroidism and taking thyroid hormone medication [10]
H. Pylori Infection
  • Thyroid antibodies (TPO) were found more often in patients with H. pylori infection (52.3%) than in patients without H. pylori infection (7.8%) [11]
  • A significant association was found between H. pylori infection and Graves’ disease [12]

While these studies only show association and not cause, collectively, they suggest an overall pattern of gut disturbances in thyroid patients.

Thyroid Symptoms or Gut Symptoms?

Symptoms like fatigue, brain fog, depression, and anxiety, and headaches aren’t unique to hypothyroidism. In fact, they are also symptoms of gut health conditions. Consider these research highlights:


  • A meta-analysis of 17 studies found that more than 50% of IBS patients have symptoms of fatigue [13]
  • 68% of patients with suspected non-celiac gluten sensitivity reported tiredness and lack of well-being [4]
  • Treating leaky gut reduces fatigue and other symptoms in patients with chronic fatigue syndrome [14]
Brain Fog
  • Subjects with brain fog are more likely to have SIBO when compared to those without brain fog [15]
  • 38% of patients with suspected non-celiac gluten sensitivity reported brain fog [4]
  • Patients with Crohn’s disease frequently complain of cognitive difficulties [16]
Depression and Anxiety
  • A systematic review involving 22,842 subject found IBS patients were three times as likely as healthy subjects to have either anxiety or depression [17]
  • 39% of patients with suspected non-celiac gluten sensitivity reported anxiety [4]
  • Migraine patients are more likely to have IBS [18]
  • 54% of patients with suspected non-celiac gluten sensitivity reported headaches [4]

This overlap between gut symptoms and thyroid symptoms leads to a common problem for thyroid patients. Once you get a thyroid diagnosis, healthcare practitioners tend to focus exclusively on thyroid treatments and stop considering other options. The result is that you end up chasing various thyroid solutions, without ever resolving your symptoms.

Thyroid medication can be very helpful for improving your thyroid hormone levels, however it doesn’t always lead to symptom resolution. As we see regularly in the clinic, healing your gut issues is the missing piece for many thyroid patients.

Research supports using a gut-focused approach to treating thyroid patients. Let’s take a closer look.

Gut Treatments Improve Thyroid Health

The research clearly shows that when you treat gut conditions, thyroid health also improves, sometimes dramatically. One small study found an astounding average drop in TPO antibodies of 2,029 when patients were treated for H. pylori gut infections [19]. Treating H. pylori has also been shown to improve TSH levels [7, 8, 20].

Treating Blastocystis hominis (a gut pathogen) has been shown to reduce inflammatory markers, thyroid antibodies, and TSH levels [21].

Identifying and removing food triggers can be helpful for some thyroid patients. 

  • One study found that lactose restriction led to significant decreases in TSH levels for thyroid patients with lactose intolerance [22]. 
  • Another study found that a gluten-free diet improved the effects of thyroid medication for thyroid patients with atypical celiac disease [23].

Research also shows that gut treatments improve thyroid-like symptoms, including 

  • Fatigue [14, 25, 26
  • Mild to moderate depression [27]
  • Anxiety [28]

All of this evidence suggests that if you have a thyroid diagnosis, it’s worth supporting your gut health as a means to reducing your symptoms and improving your thyroid health.

Gut Problems Are Two to Ten Times More Likely Than Thyroid Problems

Misdiagnosis of thyroid conditions is sadly common [29, 30]. For a surprising number of patients, an incorrect thyroid diagnosis creates a needless distraction that gets in the way of identifying the true problem and resolving symptoms. Research confirms what we frequently see in the clinic:

  • Gut conditions are much more common than hypothyroidism [31, 32, 33].
  • Gut conditions are frequently underdiagnosed [31, 34].
  • Hypothyroidism is frequently over diagnosed [29, 30].

An estimated 10-15% of people in the USA have IBS, but only about half of these cases have been diagnosed [31]. In one survey of patients with GI complaints, 43.1% of subjects who met the Rome IV criteria for IBS had never been diagnosed [32]. Beyond IBS, research suggests that nearly 40% of adults worldwide have a functional gastrointestinal disorder [34].

Compared to 10-40% of people with IBS or functional gastrointestinal disorders, only 4.6% of the US population is hypothyroid [33]. One study showed up to 60% of patients may be taking thyroid hormone replacement unnecessarily [30].

A Healthier Gut = Better Absorption of Thyroid Medication

Another benefit of better gut health is that it may result in better absorption of thyroid medication.

Several studies found that gut infections, food sensitivities, low stomach acid, and other gut conditions can impair absorption of standard thyroid hormone medication [20, 22, 23, 35].

In one study, 21% of patients were able to reduce their thyroid medication dose after H. pylori treatment [8].

Probiotics are a great starting point for improving your gut health. In another study, thyroid patients who took probiotics were able to reduce their thyroid medication dosage [24].

Probiotics help with thyroid medication absorption because they improve the balance of microorganisms in your gut, reduce gut inflammation and help to heal the gut lining [36, 37, 38, 39, 40].

Gut Health Tips for Thyroid Patients

If you are taking thyroid medication and still have thyroid-like symptoms, improving your gut health may make a big difference. Improving gut health may also help those who have thyroid-like symptoms but test negative for a thyroid condition.

The best way to begin healing the gut is with a whole foods, anti-inflammatory diet and probiotic supplements. A paleo-like diet is a great anti-inflammatory diet template that works well for most thyroid patients.

Triple Probiotic Therapy is a therapeutic, multistrain approach that we developed in the clinic through years of trial and error with prescribing probiotics. It includes research-validated probiotic strains from all three major probiotic categories:

  • Lactobacillus & bifidobacterium species 
  • Saccharomyces Boulardii (a probiotic fungus)
  • Bacillus species (soil-based probiotics)

We know from research that multistrain probiotics are more effective than single strains [41, 42, 43]. We’ve also learned from patients that trying random probiotic products isn’t always helpful. For many patients who have tried probiotics in the past, Triple Probiotic Therapy achieves significantly better results.

We recommend starting your gut healing journey with a 3-4 week trial that combines an anti-inflammatory diet and Triple Probiotic Therapy. Any level of symptom improvement during this trial period is an indication that your gut health is improving. If you see improvement and are starting to feel better, continue with this approach.

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For some patients, dietary improvements and probiotics will be all the treatment needed to completely eliminate thyroid-like symptoms. Other patients may need to take additional steps, such as:

Our clinic can help you navigate more advanced steps of gut health treatment.

As your gut becomes healthier and your symptoms resolve, you may start to absorb thyroid medication better. Lab tests and a bit of fine tuning with your health provider can help to optimize your medication dose. The majority of patients do not need alternative thyroid medication, such as combined T4/T3 therapy.

Case Studies

My clinical experience parallels the research results I have shared in this article. Here are a couple of patient stories that show how treating the gut can resolve stubborn thyroid symptoms.

Amy’s story

Amy was misdiagnosed with a thyroid condition and spent a year and a half trying to fix her thyroid.

Paige’s story

Thyroid medication alone didn’t resolve Paige’s symptoms.

Don’t Let This Happen To You

Many thyroid patients suffer needlessly with unresolved symptoms, spending energy and money chasing thyroid treatments that don’t work.  If you are struggling with stubborn “thyroid” symptoms, a change in focus can help.

Thyroid treatments will never fully work when the root cause of your symptoms is a gut imbalance. Simple interventions to improve gut health can lead to quick and effective symptom relief for thyroid patients. Start with an anti-inflammatory diet and a therapeutic probiotic protocol.

➕ References
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