Thyroid disorders and autoimmune diseases are on the rise dramatically these days and they are a common phenomenon in most modern societies. But have you ever thought that the information you are receiving and the kind of thyroid or autoimmune treatment you are following is not enough or is not efficient? Additionally, how can you consider any treatment to be efficient if your health is still poor and new negative symptoms keep appearing in other areas of the body? The reality is that without exactly knowing what is going on in your body, you can’t take proper decisions about your health. Here is some essential information you should understand about thyroid disease and autoimmune conditions.

Hypothyroidism: Symptoms and Causes

Hypothyroidism is the most common thyroid disorder. There are many causes for this condition, but among the most common are: the pituitary gland not sending enough TSH to the thyroid, or a thyroid that doesn’t produce enough T4 and T3 for the cells. Deficiencies in essential nutrients for the thyroid like selenium, zinc, iron, vitamin D or B vitamins, as well as thyrosine and iodine are at the core of hypothyroidism.

But most of the times, hypothyroidism appears following the autoimmune disease Hashimoto thyroiditis, when it has progressed far enough to destroy the thyroid tissue.

Hypothyroidism leads to a slowing down of metabolic processes and this will in turn lead to numerous symptoms such as fatigue, weight problems, cold hands and feet, constipation, poor concentration, low libido, infertility, depression, slow cardiac rhythm, low body temperature.

Hashimoto Thyroiditis: Symptoms and Causes

Autoimmune illnesses are where the immune system has lost control and started to attack body tissue which can be the thyroid tissue, the intestines, or it can be the pancreas, the skin, brain or other organ.

But regardless what organ is under attack, the real cause is a dysfunctional immune system, not the tissue or organ that’s being attacked! So it makes sense to treat and reverse this condition through proper balancing of the immune system.

Hashimoto thyroiditis can be present in the body for years without you knowing, because the symptoms are diverse; they appear and disappear or progress in time and they are not necessarily part of a certain category. One person may have mainly skin problems, another might be more fatigued, depressed or irritable. But the most common symptoms are: weakness, tiredness, weight gain, hair loss, constipation, irregular menstrual cycle, cold sensitivity, muscular cramps, muscle and joint pain, memory loss, depression and dry skin.

Leaky Gut

If you suffer from an autoimmune disease then you probably also suffer from leaky gut, which appears when the tight junctions that maintain the integrity of the intestinal wall become way too large. This allows undigested food particles, microbes and toxins to enter the blood stream. These are perceived as invaders by the immune system, and will lead to a substantial rise in inflammation. The immune system will start losing control and might eventually start attacking its own body tissues.


Gluten contributes to autoimmune disease through the alteration and inflammation of the digestive system and stress on the immune system. Gluten strongly contributes to leaky gut because it releases zonulin, a chemical that enlarges the junctions of the intestinal wall. The gluten protein has a similar structure with the one present in some bodily tissues, especially the one in the thyroid gland. This can lead to “molecular mimicry”, where the organism mistakenly attacks its own tissues thinking it is gluten protein.

Inflammatory foods that need to be avoided by Hashimoto sufferers are pastry goods, sweets, processed foods, but also cereals, legumes, nuts, seeds, night shade vegetables, eggs, dairy and caffeine. These over-stimulate the immune system and further contribute to leaky gut.


Hidden or undetected infections with bacteria like E.coli, mycoplasma or Borrelia (causing Lyme disease), viruses like Epstein Barr, Herpes Simplex and other toxins can all contribute to the development of immune diseases. Chronic infections cause an imbalance in the immune system, which is now more vulnerable to the attacks of pathogens and more susceptible to attack its own tissues.


Chronic stress affects the immune system, leading to long term inflammation, which won’t stop as long as stress continues. Once the autoimmune response is present, stress will exacerbate the reaction. And most autoimmune illnesses are initiated by chronic stress or unresolved emotional trauma.


High toxicity needs to be considered in autoimmune diseases. Many people with Hashimoto are sensitive to mycotoxins for example, which are highly volatile compounds produced by toxic mould, which disturb the immune system. Heavy metal toxicity is very real and common these days and needs to be addressed. Heavy metals accumulate in vital organs, imbalance their functions, replace nutritional minerals and block the enzymatic activity creating biochemical chaos.

Genetic Mutations

HLS is a class of genes found on the cell’s surface whose function is to connect protein fragments to antigens in order to be recruited by the lymphocytes. HLA genetic variations are a risk factor in developing autoimmune diseases. HLA gene variation will influence the immune response to a variety of substances such as toxins, antigens, vaccines, moulds, biotoxins, viruses and pathogens.

Also, other genetic mutations like MTHFR significantly reduce the ability to metabolise certain nutrients which contribute to methylation, such as B vitamins, choline, folate and others. With such mutations, the organism cannot properly utilise key nutrients.

Methylation plays an important role in detoxification (which is essential with autoimmune diseases), utilizing B1 and B6 vitamins, folate in glutathione formation (the body’s primary antioxidant), cellular immune activity and neurotransmitter function. Genetic mutations or dysfunctional methylation enzymes can imbalance this process, leading to hormonal and inflammatory dysfunctions. Some of the enzymes / methylation genes are: MHFR, MTRR, PEMT, COMT, MAO-ACBS, NOS, FUT2. With testing you can find out the status of these mutations and how these can affect your health in correlation with the dysfunctions and imbalances present in your body.

Nutritional Deficiencies

Nutritional deficiencies are also essential in the way autoimmune illnesses appear and evolve. Vitamin D has a very important role in the immune system and deficiencies are very common. Vitamin D prevents autoimmunity through the stimulation of regulatory T cells, which are charged with differentiating between invading cells and the body’s own cells.

Essential omega 3 fatty acids contribute to the activation of B cells and the selection of antibody production which can reduce the inflammatory response. B vitamins control the immune function, hormones, mood, sleep, nerves, circulation and digestion. When you have a deficiency of B12 vitamin for example, the white blood cell count is low, and this weakens your immune system, making it susceptible to aberrant attacks.

Selenium is essential for the regulation of excessive immune response and chronic inflammation in autoimmune diseases. It is also essential for a well-functioning thyroid. The enzyme that transforms T4 (the inactive form of thyroid hormone) into T3 (the active form of thyroid hormone) is dependent on selenium. So without a sufficient amount of selenium in the body the hormones are blocked into their inactive state, generating hypothyroid symptoms.

A sufficient level of selenium can prevent and ensure the reverse of thyroid autoimmune illnesses. The process the body uses to transform iodide from food into iodine produces hydrogen peroxide. This is a pro-oxidant and alters thyroid cells, which can initiate an autoimmune response. Selenium neutralises the hydrogen peroxide and contributes to reducing thyroid antibodies.

Zinc also plays an important role in T4 – T3 conversion. When zinc is low, the hypothalamus can’t correctly calculate the level of thyroid hormones, in order to raise the production of these when they are insufficient.

Magnesium deficiency can cause a high production of pro-inflammatory citokines, which raise the overall inflammation in the body, contributing to autoimmunity.

Iron deficiency is very common in hypothyroidism sufferers. The enzyme that transforms iodide into iodine in order to combine with thyrosine and form thyroid hormones is iron-dependent. Iron is also necessary for the T4 – T3 conversion.

The heme molecule, the most important component of haemoglobin protein, is bound to the thyroid peroxidase enzyme. This together with thyroglobulin has a key role in the iodination of L-tyrosine, an essential process in the formation of thyroid hormones. Insufficient iron affects haemoglobin leading to low thyroid hormone synthesis. Because the thyroid hormone alters the rate of heme oxidation in the liver, the low thyroid function can generate a vicious cycle where iron deficiency is involved.

Supplementing with iron is not recommended for several reasons. If there is digestive insufficiency present, such as lack of gastric acid (very common in autoimmune sufferers!), iron can’t be absorbed properly.

Many forms of iron available can’t be properly absorbed by the body. Iron is a powerful pro-oxidant, so the body is using a few mechanisms to prevent free iron to be released. In situations where there is increased oxidative stress and high activity of free radicals, the cells are intelligently programmed to rapidly break down the heme form, in order to prevent free iron from entering the blood stream. Iron supplementation can add to this pro-oxidative activity, especially when this is not bound to proteins. So with hypothyroidism, where at least a moderate level of oxidative stress is usually present, the iron supplementation will only raise the oxidation activity.

The type of iron necessary for the thyroid and that is correctly metabolized by the body is the one found in food, especially in animal products.

Iodine is a critical nutrient for the optimal functioning of the thyroid, and deficiencies are common. However this doesn’t necessarily happen because of insufficient iodine from the diet, but rather because of the iodine bio-unavailability in tissues. This usually happens because of environmental toxins: bromide, fluoride, chlorine, halogens, heavy metals which all block iodine absorption.

That’s why knowing the cause is so essential – detoxifying from toxic compounds and not necessarily supplementing with iodine, especially because many people react negatively to this.

One of the major factors influencing T4 to T3 conversion is glutathione, which is the most powerful antioxidant in the body. Its ability to prevent free radical damage is well-documented, as is its ability to detoxify numerous heavy metals, chemicals, xenobiotics and carcinogenic substances. Inadequate reserves of glutathione has many causes, including oxidative stress and cellular toxicity.

Gluthatione is a “redox” molecule. This means that it passes through a cycle of oxidation and reduction. When intracellular-reduced gluthatione (GSH) is consumed, it loses its electrons and becomes disulfide glutathione (GSSH). It can get back its electrons and it can transform into usable form only in the presence of an electron donor. The primary donor is NADPH (nicotinamide adenine dinucleotide phosphate).

A person with a high level of oxidation, “consumed” gluthatione, and a low level of usable, bio-available glutathione is a person that presents a significant level of cellular toxicity and oxidative stress. There are studies showing a direct correlation between a better T4 – T3 conversion through usage of NADPH and glutathione. This aspect can confirm that oxidative stress and insufficient essential antioxidant reserves like gluthatione are at the core of inadequate T4 – T3 conversion.

Functional vs Conventional Analysis of Thyroid Markers

In the conventional medical system, autoimmune diseases are not recognised as illnesses of the immune system. To suffer from Hashimoto and to take drugs for the thyroid is the classic example of allopathic medicine that treats an organ exclusively through the suppressing of symptoms.

Additionally, if you suffer from an autoimmune disease like Hashimoto, you might receive one treatment from your endocrinologist, another treatment from you dermatologist if you have skin issues, and another from a gastroenterologist if you suffer from Crohn, Coeliac disease, and so on …You will end up consulting a ton of doctors, who will all prescribe different treatments individually and none will consider balancing your immune system or discovering the causes of your autoimmune disease; addressing these is needed for real and long term healing.

In contrast, functional and integrative medicine sees the body as a whole and believes that the health of one bodily system also affects the health of the others. So the focus is on balancing your immune system by detecting causes and imbalances that led to aberrant functions, and eliminating these in a systematic, efficient and non-invasive way.

Another essential aspect is the analysis of thyroid markers, which doesn’t usually include the complete panel, like Free T4, Free T3, Anti-TPO and TgAb. This is extremely important because lots of times the true diagnostic is missed, as are other potential autoimmune diseases which might develop.

The biggest quantity of thyroid hormones are represented by Total T4, which will transform into Total T3 and then into free thyroid hormones, FreeT4, FreeT3. So Total T4 and Total T3 can provide information about what the thyroid gland produces, which is useful. But the quantity of bio-available hormones is also very important to know, because these are the ones active in the tissues. So this is the information which will determine the metabolism and function of thyroid hormone.

Also, the Anti-TPO marker is necessary to establish if an autoimmune illness is present or not. The thyroid peroxidase enzyme is present in all thyroid cells and it expresses on the surface of these. Together with thyroglobulin, this enzyme has a key role in L-tyrosine iodination, an essential process to produce thyroid hormones. From a functional point of view, a value higher than 10 IU/ml of Anti-TPO suggests the immune system has already started to attack the thyroid gland.

Case Study

Below is a real case study of a person I’m working with at the moment which demonstrates the information presented above.

Female, 65 years old, presenting with following symptoms: irritability, inefficient digestion, sensibility to changes of weather, knee pain, insomnia, sweet cravings, a little overweight.

Initial analysis: complete blood work, including complete thyroid panel (T3, T4, FT3. FT4, TSH, Anti-TPO) with functional references for interpretation.

Markers’ values:

TSH: 3.01 IU/mL

Total T4: 7.45 ug/dL

Total T3: 140 ng/dL

Free T4: 1.18 ng/dL

Free T3: 2.81 pg/mL

Anti-TPO: 203 IU/mL

Scenario no. 1. If the person had been tested only for TSH, which is what usually happens, she would have found out that this marker is slightly elevated, which is mostly ignored in conventional medical practice. The “damage” is not that big yet to prescribe a treatment.

Scenario no. 2. If the person had been tested only for TSH, T3, T4 and/or FT3 and FT4, she would have found out that TSH is slightly elevated, FT3 is low and the other markers are normal. (And this is only if the markers had been interpreted functionally, not pathologically!) So it’s possible for the diagnostic to be hypothyroidism, but it’s not guaranteed, because of the large references ranges used by the labs.

Scenario no.3. The analysis of all thyroid markers including Anti-TPO revealed that the person has a slightly elevated TSH, FT3 low and high Anti-TPO, which suggests low thyroid function and the presence of autoimmune processes (in this case Hashimoto disease).

Note: the above analysis doesn’t represent a diagnosis and shouldn’t be interpreted as such. The functional interpretation of blood work is used to detect certain tendencies, biochemical and nutritional imbalances, which can develop into diseases later if not resolved.

This information is offered for educational purposes and shouldn’t be used as a medical advice, diagnostic or treatment.

Integrative, Functional and Efficient Solutions for Healing

A correct diet, detoxification and re-establishing biochemical balance are essential aspects when addressing thyroid and autoimmune disease. As with all illnesses, the triggers and hidden causes might be different in each person. If action is directed only towards the suppressing of symptoms, you can’t ensure real healing. To prescribe lifelong medication for a thyroid autoimmune disease won’t make the gland function better. It will only act as a substitute for what the thyroid is not able to provide anymore, while likely causing negative effects in other areas of the body.

Also, there is no one size fits all when we talk about diet, and this is essential in any healing process. No diet or treatment will work for everybody. Biochemical individuality is present in all cells of the body.

So what is essential is supporting the body in a holistic and non-invasive way. This means figuring out one’s nutritional, genetic and biochemical requirements and detecting the causes of the dysfunction, rather than “treating” the thyroid.