Hashimotos and The Gluten Connection

gluten thyroid problems

By Dr. Justin Marchegiani

Hashimoto’s disease, Hashimoto’s thyroiditis is an autoimmunedisease, a disorder in which the immune system turns against the body’s own tissues. In people with Hashimoto’s, the immune system attacks the thyroid. The thryoid gland is located in the front of your neck. It makes hormones that control metabolism.

Did you know that up to 90% of thyroid conditions are autoimmune in nature? This is a really important concept to master because in the conventional medicine community whether someone’s thyroid condition is autoimmune or not the treatment doesn’t change. I know, this makes me want to pull my hair out, too! I have an autoimmune thyroid condition myself, and knowing whether or not your thyroid condition is autoimmune can make all the difference in the world.

If you want to get your thyroid assessed click here!

Gluten and Autoimmune Connection

Eating gluten can increase your body’s production of thyroid antibodies! Essentially when you’re increasing your thyroid antibodies because you are eating gluten, you are destroying your thyroid gland faster. As your thyroid tissue gets destroyed, your ability to produce more thyroid hormone also drops. The longer you’ve had an autoimmune thyroid condition, the greater chance you will need some type of thyroid hormone intervention in the future. The sooner we can intervene when someone has Hashimoto’s, the better chance the person can keep their full functioning thyroid gland.Thyroid and Gluten Damage

This is what I tell my patients who have an autoimmune thyroid condition. It’s also what I practice myself!

“Imagine every bite of gluten literally burning up a piece of your thyroid tissue that you will never get back!”

If you’re serious about having good thyroid function, it becomes a must for you to give up gluten. I always recommend patients get their thyroid antibodies checked before they ever think about splurging on gluten. Gluten free alternatives are not recommended until the patient gets healthy again. I have seen many patients get their thyroid antibodies down to undetectable levels following the functional medicine strategies mentioned in this blog post.

With some sensitive individuals it’s shown that you have to be off gluten for at least six months for your gluten antibodies to be undetectable. What this means is a little bit of gluten can go a long way in destroying your thyroid health!

Gluten is strongly connected with autoimmune thyroid conditions and celiac disease. Research has found that many patients were subclinical celiac have Hashimoto’s (an autoimmune thyroid condition). Researchers are also finding more people with sub-clinical celiac disease. There are many reasons why this is so, many of the dietary and environmental stressors are causing a phenomenon known as leaky gut. Leaky gut is when the gastrointestinal tight junctions open slightly and allow undigested food particles (antigens) to make their way into the bloodstream.

Many people who have an autoimmune thyroid condition have a significant chance of having a second autoimmune condition. This is known as polyglandular autoimmune syndrome, and it is closely connected with gluten. Gluten stimulates the compounds on zonulin which acts as a zipper, unzipping the tight junctions allowing food and bacteria into the bloodstream.

leaky gut

False Negative Lab Test For Hashimotos

Over 30% of the time lab work can be false negative for Hashimotos thyroiditis. I strongly recommend multiple antibody tests along with a thyroid palpation to rule out Hashimotos. I refer out patients for a thyroid ultra sound if any swelling or nodules are detected on palpation.

In functional medicine, we use more sensitive lab ranges that can help us pick up potential problems before they are found via a standard lab reference range. For instance, TPO antibodies that are greater than 15 IU/ml would make me very suspicious of Hashimotos.

The true gold standard diagnosis is a tissue biopsy to detect Hashimotos. I try to avoid this type of diagnostic method due to its invasive and inflammatory nature. Following the above recommendations can be enough to get you the answers you need.

When in doubt, cut gluten out of your diet, anyway! There is a small chance of slipping through the cracks regarding Hashimotos diagnosis. It maybe an inconvenience in the short run, but a greater inconvenience is not having an optimally functioning thyroid gland.

Thyroid Treatment Options

What you’ll see when comparing the two options is the functional medicine treatment plan is far more in depth and actually address the underlying cause (physical, chemical and emotion stressors) of the disease.

The conventional treatments typically only treat the symptoms and doesn’t come anywhere close to fixing the root cause. The conventional treatments work really well with physicians that only have 3 to 5 minutes to treat a patient (the current insurance model). There isn’t an even enough time to talk about gluten, one of the prime simulators for an autoimmune thyroid condition.

Most patients have to step outside of the conventional insurance model to truly get well.


  • Medications: Synthetic T4 most of the time (synthroid or levothyroxine), sometimes synthetic T3 (cytomel).

Functional Medicine:

  • Nutrition: Dietary interventions including an autoimmune paleo diet that is nutrient dense, anti-inflammatory and low in toxins.  Addressing nutritional deficiencies such as zinc, magnesium and selenium. If you have an active autoimmune thyroid, it’s important to avoid taking iodine in the beginning. There’s a time and a place when it comes to Iodine… More on this topic later.
  • Hormones:  When an autoimmune thyroid condition is present, there tends to be some level of adrenal fatigue or female hormone imbalance as well. Running blood or salivary testing to assess the function of the other hormonal systems is very important!
  • Digestion: Patients that have an autoimmune thyroid also tend to have poor digestion. As thyroid function decreases, so does the body’s ability to make stomach acid. When stomach acid gets lower, it’s harder for us to break down proteins and minerals. As you can see, there’s a vicious cycle starting here. Without enough healthy proteins and minerals, it’s hard to have healthy thyroid function.
  • Infections: There are a handful of infections in the scientific literature connected to Hashimoto’s. A few include H. PyloriYersinia,  Epstein-Barr and Lyme disease. Clinically speaking, when we remove these infections, antibodies drop and patients begin to feel better.

If you want to get your thyroid assessed using the functional medicine model, click here!

Below is an example of a patient who had infections that were removed like the ones above. These patients also made changes addressing blood sugar stability as well as removing gluten from their diet. Look at the 95% drop in thyroid antibodies that occurred over a 1 year time frame.

drop in thyroid antibodies

How Does Molecular Mimicry Work?                                                       

There are amino acid sequences on these antigens (foreign particle) that are similar to other tissues in the body. Our immune system reads these antigens by the sequence of its surface proteins. It’s kind of like getting pulled over by a policemen that is out looking for a similar make and model of  the car you drive, because a suspected criminal was seen driving that same car earlier that day.

Foods like gluten can easily cause your immune system to start attacking the thyroid gland, brain, intestinal tract (celiac, chron’s, ulcerative colitis) or other nervous system tissue based on similarity and genetic predisposition.

There’s a good deal of research showing that autoimmune disease cannot occur without a leaky gut. This is why anyone with a chronic illness needs to have their gut checked.

Clicker here to get your gut checked!

Gluten and Cross Reactivity

When these proteins have a similar shape to other proteins, cross reactivity can occur. These proteins have the ability to bind into other receptor sites just like with casein and gluten. As you can see by the picture below, the shape of the antigen can be enough to confuse the immune system.

cross reactivity

Foods like casein from dairy products can cause the immune system to start attacking the pancreas. Casein can also cross react with gluten to! Cross reaction is where the immune system starts responding to other proteins as if they are gluten. This is the reason why some people who only remove some grains from their diet may not recover fully. The consumption of other cross reactive foods outside of gluten can be enough to prevent your thyroid from healing.

If you need help making changes with your diet, lifestyle and hidden stressors to help get your thyroid back on track feel free and click here for a complimentary evaluation.

Hypothyroidism: A Natural Approach To Healing

Hypothyroidism Natural Approach To Healing

By Dr. Justin Marchegiani

Most people I meet with thyroid symptoms (hypothyroidism) feel: fatigued, cold hands, cold feet, thinning hair, over weight and depressed. These symptoms can be fixed, and are typically not alleviated by conventional thyroid medications.

Conventional thyroid treatments typically only involve synthetic T4 (inactive thyroid hormone), which many individuals have a difficult time converting into T3 (active thyroid hormone).

There are many different factors that may prevent you from making this conversion.

A couple of these factors are the following:

 Hypothyroidism Common Factors

  • Adrenal fatigue

Cortisol from the adrenal is need to activate thyroid hormone, while at the same time not enough thyroid hormone could suppress the conversion.

  • Selenium deficiency

 The 5 deiodinase enzyme this is responsible for converting thyroid hormone is selenium dependent. Any deficiency could impair the conversion.

  • Autoimmune thyroid 

    (Hashimoto’s or Grave’s disease)

The antibodies from these conditions can block the receptors for thyroid hormone.  When the receptors are blocked, thyroid hormone will not be able to do it’s job and increase the medication won’t work either.

  • Iodine deficiency

(Remember, don’t take Iodine unless you have been properly assessed by a physician to rule out an autoimmune thyroid, taking Iodine could make the problem worse!!!

Know more about iodine issue by clicking here.

  • Anemia

This could range from a B12/Folate anemia all the way to a iron based anemia.

  • Infections

Chronic infection could create excess inflammation which could impair hormone conversion.

  • Blood sugar swings

Eating refined sugars, food allergens and high glycemic carbs with out enough high quality protein and fat could exacerbate blood sugar swings which can affect thyroid hormone balance.

  • Low stomach acid

Stomach is need to break down protein and ionize minerals that are important for thyroid health. Many times infections are to blame for low stomach acid.  You need to get tested to rule out the infection connection!


Hypothyroidism Root Cause

Whether you have an autoimmune thyroid condition like 90% of the population conventional medicine doesn’t seemed to be to concerned because their treatment doesn’t change either way. It’s time medicine evolve and start providing customized care based on the patients individual needs.

At my clinic it’s amazing how fast patients turn around and start feeling better once the underlying causes of their thyroid hormone imbalances are addressed!

If you want to get your thyroid fixed, schedule a complimentary consultation by click here!

Gluten’s Devastating Effects and How To Test For It

Glutens Devastating Effects And How To Test For It

By Dr. Justin Marchegiani

Gluten sensitivity is a state of genetics, just like your genes cannot be changed, what we have control over is the expression of our genes. Gluten is one of those food products our genetics have not adapted to well.  If you are a person that have genetics that predispose you to gluten sensitivity, the way  in which you can control  how your genes are being expressed, is to avoid gluten.


Lets review some terminology that is used to describe people who react to gluten and or grains. Many people with gluten sensitivity can be gluten intolerant or have a gluten allergy as well.

The terms “allergy” and “intolerant” have come to mean different things in conventional medicine, so the more excepted terminology in gluten circles like this is the term “sensitivity”.

Sensitivity is referring to the fact that your immune system is hyper responsive to the gluten proteins. The byproduct of these hyper-immune responses is inflammation and if prolonged, autoimmune conditions are a strong possibility.

Gluten Allergy

Refers to your immune system creating an IgE immune response (anaphylactic in nature) to the gluten protein, these allergies are inborn and are usually known at birth.  With new cutting testing we know allergies can also be delayed in nature via an IgG or IgA response; this is closer to what we see in gluten sensitivity.

Gluten Intolerance

Refers to the inability to break down the gluten proteins in the digestive tract. Just like with lactose intolerance, some individuals have a difficult time breaking down lactose (milk sugar), but with specific enzymes (like lactaid) this is possible. Most people who are gluten sensitive have a difficult time breaking gluten down too, but taking enzymes alone will not be enough to avoid the inflammation and autoimmune destruction from consuming it.

In science today gluten sensitivity has been primarily connected  with celiac disease, so the misconception is if you don’t have celiac disease, you don’t have gluten sensitivity.

This couldn’t be further from the truth! The testing used to diagnose and assess celiac disease can miss many people. Essentially you can have all of the telltale signs and symptoms of gluten sensitivity or celiac disease, and still be misdiagnosed.

The typical mainstream diagnosis for celiac disease is a sample of your micro-villi from your small intestine via endoscopy. The micro-villi have to be worn down 80% for you to be considered celiac.

There are a couple problems with this diagnosis criteria:

Glutens Problems And Diagnosis

1. What if we do not collect a sample that was affected by gluten?

2. What if the  micro-villi have not been worn down 80%?

This method is analogous to pulling a bucket of water out of the ocean, examining that there is no fish in the bucket and then concluding the ocean must have no fish. This may not be a perfect analogy, but I think you know what I’m getting at.

There are other blood tests that can be used to confirm celiac disease. These blood test includes transglutaminase antibodies, endomyseal antibodies, deamidated gliadin as well as gliadin antibodies. If you come back positive with one of these test markers, you can be confident that you have celiac disease. The problem is, many individuals come back negative with these markers and still may have  gluten sensitivity.

This is where genetic testing comes into play, if you have a gene that predisposes you to gluten sensitivity it’s just a matter of time till those gene expresses itself. The more physical, chemical and emotional stress you  are under, increases the chance that your gluten sensitive genes will react and start creating symptoms. As you well read below, the symptoms for gluten sensitivity are all over the map!

Want to know if you have gluten sensitivity? Click here.

What are the best tests out there?

Glutens Tests

I think genetic testing is a good tool to assess if you have the genes for gluten sensitivity.  The problem with other testing is it’s very easy to have false negative result (the test comes back negative  but in reality you may still have gluten sensitivity). If you come back with a gluten sensitive gene, you can be confident that it’s just a matter of time before that gene expresses itself if you keep eating gluten.

The primary genes that are involved in celiac disease are HLA-DQ2 and HLA-DQ8.  There are other HLA-DQ genes involved as well; HLA-DQ 1, HLA-DQ 3 and HLA-DQ 7 are also genes that predispose you to gluten sensitivity.

When you’re looking at genetics such as HLA-DQ testing, you get one HLA-DQ gene from each parent.   If you receive two HLA-DQ 2’s or two HLA-DQ 8’s, this increases the risk of celiac disease (the same goes for gluten sensitivity). According to the genetics, the only people that are immune to gluten sensitivity are people with the genetic sub-types HLA-DQ 4 (which are less than 1% of the population). There needs to be more research done validating gluten sensitivity and its connection with the genetics (1).

The percentage estimates surrounding gluten sensitivity regarding the population are a point of contention among  experts. Dr. Alessio Fasano at the University of Maryland medical school, who is a pioneer in gluten research, feels that only 6 to 7% of the population are gluten sensitive; while Dr. Ford a pediatrician in New Zealand and the author of the book “The Gluten Syndrome,” believes  30% to 50% of the population are gluten sensitive.  According to Dr. Kenneth Fine over 50% of the population is gluten sensitive. Either way you look at it, the new estimates that are coming out surrounding gluten sensitivity are showing a significant increase than the original 1% estimates of celiac disease.

The information that we have now shows the majority of the population are gluten sensitive. The problem with gluten sensitivity, is the majority of symptoms that come from gluten are not necessarily correlated with digestive issues (symptoms that are gastrointestinal in nature like bloating, gas, diarrhea and IBS). With gluten sensitivity you are actually 8X more likely to have extra intestinal symptoms, (symptoms not related to the gastrointestinal tract, like headaches, depression, lupus and thyroid disease).  This is the main reason why gluten sensitivity is so easily glossed over today.

Most patients with gluten sensitivity complained of 2 or more symptoms (2).

gluten symptoms

The symptoms of gluten sensitivity

Celiac disease is a form of gluten sensitivity, so essentially if you have celiac disease you are gluten sensitive. At the same time if you are gluten sensitive, you don’t have to necessarily have celiac disease.

There are many common manifestations of gluten sensitivity, I call this the web of gluten sensitivity:

This includes:

Various anemia’s, type I diabetes, Hashimotos and other thyroid diseases, fibromyalgia, chronic fatigue syndrome, lupus, there is gut infections, skin issues (psoriasis, eczema, dermatitis herpetiformis), psychological and mood disorders (schizophrenia, depression).

Gluten Sensitivity

I challenge you to Google scholar or pubmed search gluten or celiac disease with any disease of your choice. You will see many results come up in your search, proving the connection cannot be ignored.

My favorite method to assess for gluten sensitivity!

The problem with many of the tests that are out there, is that similar information can be received through a simple elimination provocation diet (this is where  inflammatory foods are cut out for a period of time and then added back in). The only time I conduct testing on patients, is if patients are resistant to changing their diet. Then the lab test be very useful, because they can quantify to the patient in an objective manner that these issues are real. Some people  need to see that type of evidence before they cut out some of their most favorite and addicting foods!

I find almost all individuals who are suffering from some type of chronic illness benefit when they cut gluten out of their diet. The foods that contain gluten, which are all grains, tend to be very low in nutrition, have a high glycemic index and create inflammation. It’s always better to eat foods that are nutrient dense, anti-inflammatory and low in toxins.

My recommendations are for all of my patients to start off with some type of anti-inflammatory, autoimmune paleo or bulletproof style of eating. The focus with this type  of eating is to be consuming foods that are anti-inflammatory, low in toxins and nutrient dense. This allows us to put our body into a state of healing  so we can start recovering from all of the damage created by the gluten exposure. Macro-nutrient ratios including carbohydrate, protein and fat can always be adjusted to meet the needs of the patient. I deal with these macro-nutrient ratios on individual basis per patient.

What Do You Do If you Aren’t Feeling Better After Going Gluten Free?

When dealing with patients that are chronically ill,  making the above dietary recommendations may not be enough. The inflammation created from years of stress and gluten consumption, may have caused damage to your adrenals, thyroid and gastrointestinal system. This may have weakened your immune system to the point where chronic infections like parasite, bacterial, fungal and viral infections have gained a foothold. I find removing these infection can be the missing barriers that are preventing people from getting better.

If you’re not getting better  from going gluten-free,  feel free and schedule a complimentary consultation by clicking here to review what your options are.


1.A. Fasano et al. Divergence of gut permeability and mucosal immune gene expression in two gluten-associated conditions: celiac disease and gluten sensitivity. BMC Medicine 2011, 9:23. doi:10.1186/1741-7015-9-23.

2. New understanding of gluten sensitivity, Umberto Volta & Roberto De Giorgio, Nature Reviews Gastroenterology & Hepatology 9, 295-299 (May 2012).

The entire contents of this website are based upon the opinions of Dr. Justin Marchegiani unless otherwise noted. Individual articles are based upon the opinions of the respective author, who retains copyright as marked. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of Dr. Justin and his community. Dr. Justin encourages you to make your own health care decisions based upon your research and in partnership with a qualified healthcare professional. These statements have not been evaluated by the Food and Drug Administration. Dr. Marchegiani’s products are not intended to diagnose, treat, cure or prevent any disease. If you are pregnant, nursing, taking medication, or have a medical condition, consult your physician before using any products.