Thyroid & Your Gut – Hidden Cause of Thyroid Problems #2 – Gluten, Food Allergies & Thyroid

All Disease Begins in the Gut” ~ Hippocrates

Gluten, Food Allergies & Thyroid

gluten_food_allergies__thyroidSome have said health and disease start in the gut; in functional medicine we certainly feel this is true.  If I could only address one area with a patient it would be their gut.  Addressing your digestive health is the single most important action you can take.  If you have any health issue and your digestion is not perfect, than addressing your digestion should be the first thing that you do.  The travesty is gut health is one of the most common areas of dysfunction that causes thyroid problems, but gut/digestive problems are poorly addressed in our health care system.  Did I say poorly, I’m sorry let me rephrase that; they are absolutely terribly addressed for the most part.  If you read “My Story” you will learn that I was originally planning on becoming an orthopedic surgeon until I fell ill.  I had an intestinal problem that was missed by every conventional physician I saw.  It was not until I found a DC who practiced Functional Medicine that I found the answers I was looking for and got better.  This changed my life and my entire career path!  So please excuse me if I am passionate about this.


Food allergies and food intolerances are one of the most common gut related problems.  Food allergies tend to be quick reactions that cause rashes, swelling and can be dangerous.  Food intolerances are more subtle; they tend to cause low level inflammation that can cause fatigue, bloating, brain fog, hypothyroid and a myriad of other problems.  For simplicity I may occasionally be using these two terms interchangeably.  When someone has a food intolerance or food allergy reaction a few things occur.  Essentially your body does not like the particular food being ingested; gluten is the most well studied in this regard, but it applies similarly for all food allergies or intolerances.  The body perceives a food allergen/intolerant almost like a foreign invader (bacteria, parasite or virus) and sends the immune system to attack.  One of the weapons used by the immune system is inflammation.   Think of it like this, your immune cells have little guns that shoot damaging inflammation at enemies to kill them.  This is how certain anti-inflammatory agents are used to treat autoimmunity; because if you overly suppress inflammation, you suppress the immune system.  The challenge here is most pharmaceutical anti-inflammatory drugs end up causing more damage than they do good, making using them in the long term not an option.  Remember back to our section on autoimmunity?  We discussed how autoimmunity (in this case Hashimoto’s) can be caused by over stimulation of the immune system.  Well this inflammatory-immune response in the intestines that occurs when you eat foods you are allergic to is just that, a stimulator of the immune system.  So said another way, when you eat food you are allergic to you cause an immune reaction.


When this food allergy reaction occurs a few other thing happen too; remember no system operates in isolation.  This inflammatory-immune response in the intestines will also cause an elevation in stress hormones, and elevation in stress hormones further damages your intestinal lining.  As your intestines become damaged by this inflammatory-immune response your ability to breakdown and absorb food becomes compromised leading to nutrient deficiencies and toxic by product formation (toxicity).  Finally, there is also a connection to your male and female hormones.  Inflammation has been shown to cause elevations in a women’s levels of testosterone (advanced cases of this are known as PCOS) and elevations in estrogen in a male.  Additionally, as this inflammatory reaction keeps on causing a stress hormone response, it can eventually start to deplete your male/female hormones (also known as your anti-aging hormones).


Does all this seem too good (or too bad) to be true.  We will have a look at the medical references shortly but for now in summary we see a gut issues causing;

  • an inflammatory reaction
  • an immune and potentially an autoimmune reaction (we really can’t separate the two)
  • the potential to cause toxicity
  • a stress hormone reaction
  • the potential to cause nutrient deficiencies by mal-absorption
  • the potential to imbalance male and female hormones
  • in case you didn’t catch it, this is everything on our “cause list”


Please let me be clear in saying it is very likely that your gut could be playing a major role in your thyroid condition.  Don’t take my word for it though, and you probably shouldn’t take your doctors either; but how about peer-reviewed scientific evidence?  Studies have shown a differing degree of association between gut problems and thyroid.  The largest body of evidence has been published connecting celiac disease (full blown gluten allergy) and thyroid.  Let’s look at some direct quotes from the research and then connect a few dots that can be lost in translation.

“Most of the patients with positive serologic test for CD had HT (54.5%) and overt hypothyroidism (54.5%).”YELLOW

“Screening high-risk patients for CD, such as those with autoimmune diseases, is a reasonable strategy given the increased prevalence.” 1

What does celiac disease or a full blown gluten allergy do to your intestines?  Well I could give you the medical jargon of “villous atrophy, crypt hypertrophy, and Marsh II or III, but how about a picture that’s worth over 1,000 words?

What does celiac disease or a full blown gluten allergy do to your intestines?  Well I could give you the medical jargon of “villous atrophy, crypt hypertrophy, and Marsh II or III, but how about a picture that’s worth over 1,000 words?

normal_villous_architecture flattened_villous_architecture

Here we see a healthy intestine (notes the fluffy “villi” that help you absorb the life-giving nutrition from your food) and next to it an intestinal tract decimated by the negative effect of gluten in a celiac patient.  This change is mediated by an inflammatory-autoimmune response in the intestines. Now please note that most will not have this full blow visual change aka celiac disease.  However, it’s actually that majority who do not have full blown celiac disease that may be worse off.  2, 3


One of the dots we should now connect is there may be more people who have a subclinical form of “gluten intolerance” than actually have full blown celiac disease or gluten allergy.  People with the subclinical intolerance may actually have a worse overall prognosis than those with celiac.  This may be because patients with a low level intolerance never get sick enough to either a) prompt investigation b) become measurable by routine testing. 2, 3


On My Soap Box:

Some researchers are now scratching their heads and publishing commentary that reads along the lines of, ‘In the US population far more people are going on a gluten free diet than are diagnosed with celiac disease, this may indicate a subset of the population not identified by standard testing who derive benefit from a gluten free diet 2’.  I read studies like this with mixed emotions.  Partly I chuckle at the level of disconnect between some researche

rs and the general public, while at the same time I am happy that this glaringly obvious association is being noted.  You see, working with patients and their diets every day makes this connection clear, however if you are not seeing patients and/or are only dispensing pills or performing surgery this observation will elude you.  This may make you think twice before thinking the GI surgeon from Harvard is the end-all-be-all for advice regarding your gut health.  If you have a laceration to your intestinal wall, then absolutely… but if you have chronic gut problems that no specialist can figure out, you may be barking up the wrong tree as it were.  I say this not because I have any issues with the surgeon.  Surgery literally saved my life at one point.  I have great respect and reverence for it.  I say this because the person who is swept up in the mentality of House, Grey’s Anatomy, big-shinny-fancy-hospital-building-equals-intelligence-syndrome is being done a huge disservice.  This is because he or she may say to their GI specialist, “should I try a gluten free diet since I still have GI problems and no test are positive and nothing else seems to work?”  To which the doctor replies, “that is a fad” or “your tests showed you do not have a gluten allergy” or “insert dismissive remark here”.  As a healthcare consumer you should demand more.  You should demand to feel great and keep demanding answers until you get there.

OK. Dr. Ruscio, you have made a case for the association of celiac disease or gluten intolerance to hypothyroid.  How do we know going gluten free will produce a positive effect; correlation does not prove causation right?  Great question!  Demand a well articulated argument!  Sorry to do this to you again, but let’s go back for a few direct quotes from the research.


“In most patients who strictly followed a 1-yr gluten withdrawal (as confirmed by intestinal mucosa recovery), there was a normalization of subclinical hypothyroidism.” My note; gluten withdrawal means gluten free diet and mucosa recovery means their intestines health.


“The greater frequency of thyroid disease among celiac disease patients justifies a thyroid functional assessment. In distinct cases, gluten withdrawal may single-handedly reverse the abnormality.” 4


“On gluten-free diet an excellent clinical and histological response was recorded with an improvement of hypothyroidism and reduction of the thyroxine dosage.” Translation: intestines healed and people needed less medication.


“Treatment of CD with a gluten-free diet should reduce the recognized complications of this disease and provide benefits in both general health and perhaps life expectancy.” 6


As you can see, there is some extremely compelling evidence showing going gluten free can highly benefit your thyroid.  Yes, most studies are published in regard to celiac patients, but remember there are more people out there who have a lower level intolerance to gluten and who seem to be deriving marked benefit from going gluten free.


intestinesIn the section on autoimmunity you learned that when a person has one autoimmune condition they are more at risk to develop another autoimmune condition.  In this section we examined evidence connecting the gut disease celiac (aka gluten allergy) to the autoimmune disease Hashimoto’s.  So it sounds like your gut really affects your immune system.  What’s the connection?


These two pictures (also known as histological samples in geek speak) should help us see the connection.  The first picture forms a circle as you can see.  This circle is your intestines.  Wherever you see green or blue there are immune cells.  So what this is showing is your intestines are loaded with immune cells. 7



The next picture shows what’s called the tight junctions in the intestines.  Essentially the tight junctions help hold your intestinal wall cells together.  When the cells are not held together well, then you can form a condition called ‘leaky gut’.  When this happens too much of the food stuff from the intestinal track gets into the blood and can; a) cause an immune response and b) function as toxins (food particles that are not fully digestive act as toxins in the body). 7


See the squiggly lines?  They should be all scrunched up, as they are on the left side of this picture.  This means the intestinal walls cells are held tight next to one another ensuring there is no leak.  The picture on the right is showing lack of contraction (lack of scrunched up lines) that indicates the intestinal cells are not being held together tightly allowing leaky gut to occur.  The Italian gastroenterologist Alessio Fasano has found that the leading two contributors to causing this leaky gut change are firstly infections and secondly gluten. We will be talking about infections shortly.


Now what about other food allergies and hypothyroid? Well the most common food allergies are 9;

  • Gluten
  • dairy
  • soy
  • corn
  • eggs
  • nuts
  • Artificial sweeteners.


The most research has been published on gluten because celiac disease is well known and fairly problematic.  My clinical experience has showed that food allergy/intolerance tends to be somewhat individual.  This is one area where the clinical science seems to be slightly ahead of the published literature.


I hope from this conversation you can see that gut issues are massively important and can have far reaching effects.  I hope you are also starting to see how identifying and eliminating foods you are allergic or intolerant to could potentially have life changing effects.  We have covered almost everything regarding gut health, with the exception of one area; infections.  The next section will cover the infection connection.  Long story short, critters in your gut could be sabotaging your health.


Please note the next section is available through the sample chapter request box at


  1. J Thyroid Res. 2012;2012:201538. doi: 10.1155/2012/201538. Epub 2012 Mar 28.  PMID: 22545223
  2. Am J Gastroenterol. 2012 Dec;107(12):1908-12. doi: 10.1038/ajg.2012.344.  PMID: 23211856
  3. JAMA. 2009 Sep 16;302(11):1171-8. doi: 10.1001/jama.2009.1320. 19755695
  4. Am J Gastroenterol. 2001 Mar;96(3):751-7.  PMID: 11280546
  5. Horm Res. 1999;51(3):124-7.  PMID: 10461017
  6. Clin Med Res. 2007 Oct;5(3):184-92.  PMID: 18056028
  7. Am J Pathol. 2008 Nov;173(5):1243-52. doi: 10.2353/ajpath.2008.080192. Epub 2008 Oct 2.  PMID: 18832585
  8. Fissano Nat Clin Pract Gastroenterol Hepatol. 2005 Sep;2(9):416-22.  PMID: 16265432
  9. Clin Rev Allergy Immunol. 2012 Nov 16. PMID: 23229594


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