If you are struggling with thyroid issues, this page and videos will provide the kind of information you are looking for.  This page covers the key things you need to know about the thyroid gland, thyroid hormones/medication and Hashimoto’s disease: 

  • Is your doctor missing something? 
  • What your doctor does not understand about your TSH test. 
  • What you need to know about your thyroid medication. 
  • Hashimoto’s disease; its usually not a problem with your hormones. 
  • What you need to focus on if you have Hashimoto’s. 
  • Hashimoto’s it’s not just a thyroid problem. 

Is your doctor missing something?  

When your doctor runs tests for your thyroid gland they are either looking to see how well your thyroid is working on it own or what your thyroid medication is doing in your body. Unfortunately, most doctors are not very good at testing the thyroid gland and interpreting the results. This might sound like a harsh statement to make, but after reading this article you can come to your own conclusions. 

The thyroid gland can be rather complex to evaluate because so many variables can affect how it functions. We need to be able to separate a problem with the gland itself from problems with how its hormones work in your body. To top it off, most doctors are not even testing the thyroid when they run “thyroid tests.” This may sound strange, but if your doctor only runs a test called TSH, then your thyroid gland was not tested, your pituitary gland was tested. 

Does this all sound a bit confusing and possibly familiar? 

If so, then keep reading. The purpose of this article is not to belittle what your doctor is doing. I am writing this, so you are better informed about how your thyroid gland works and what your thyroid tests mean. As a functional medicine doctor, I can’t look at the thyroid gland as an isolated gland. The hormones from this gland effect every organ and system in your body. 

TSH…thyroid stimulating hormone  

Is your doctor testing your thyroid or your pituitary gland?

In most cases, insufficient testing is being done to accurately determine your thyroid hormone status. Sometimes only TSH is being tested and this provides very little information about your what your thyroid is doing. TSH (thyroid stimulating hormone) is not even produced by the thyroid gland. It is made by your pituitary gland. Doctors (including endocrinologists/hormone specialists) put far too much importance on TSH. 

Many doctors assume that if your TSH is normal, then everything about your thyroid gland is normal and in good working order. First of all, TSH is not made by the thyroid gland and TSH can be high to low for reasons not related to your thyroid gland. Only using TSH to determine thyroid status is insufficient. TSH signals your thyroid gland to make more thyroid hormone (T4/thyroxine). 

T4 hormone / thyroxine 

The main hormone made by your thyroid gland is called T4 or thyroxine. 

Thyroxine is a hormone the thyroid gland secretes into the bloodstream. Once in the bloodstream, thyroxine travels to the organs, like the liver and kidneys, where it is converted to its active form of triiodothyronine (T3). Thyroxine affects all of the body’s systems, which means proper thyroxine levels are vital for health.” 


T4 from your thyroid gland also goes to your pituitary gland where it is converted to the active form of thyroid hormone called T3. Your pituitary gland will then make more or less TSH based on how much T4 it receives and how efficiently it converts the T4 into T3…

This is where things go wrong…

This is what doctors are missing! They are not considering how well the pituitary gland is turning T4 into T3 and this significantly affects TSH levels. They are assuming that your pituitary gland is making this conversion perfectly and at the same level that everyone else does. This is entirely incorrect. 

Your TSH can go up or down even when your T4 levels remain constant. How can this happen? It all comes down to a very important group of enzymes that convert your T4 into T3. 

Enzymes turn T4 into T3 and change your TSH levels

You have 3 different enzymes that convert your T4 hormone into the stronger and more biologically active form we call T3. We call these enzymes deiodinase enzymes. 

Type 1 (D1): converts T4 into the T3 throughout your body. This T3 is what is being measured in your blood tests. 

Type 2 (D2): converts T4 into T3 in your pituitary gland. This is not measured in blood tests but does determine your TSH results. 

Type 3 (D3): this converts T4 into a form of T3 called rT3 (reverse T3) and this reduces thyroid hormone function. Too much rT3 pushes you toward low/hypothyroidism. 

You can see that the T3 levels in your body and on your blood tests are not created by the same enzyme that is creating T3 in your pituitary gland and determining your TSH levels. 

Below are some of the factors that can suppress the function of your Type D1 enzyme and cause your T3 levels to be lower on your blood tests: 

  • Inflammation 
  • Emotional stress
  • Depression 
  • Weight gain 
  • Autoimmune diseases
  • Chronic fatigue 
  • Chronic infections 
  • Chronic pain 
  • Insulin resistance (too much insulin from the pancreas) 
  • Nutritional deficiencies 
  • Poor digestive health 
  • Toxins 

When this happens, your TSH may be normal and your T4 may be normal but your T3 will be lower than it should. 

The D1 enzyme also tends to be more active in men than in women, which is another reason it is more common to see low T3 in women than men.

“T3 is biologically the most metabolically active hormone (3-4 times more potent than T4)”


The very same factors listed above that can reduce the function of the D1 enzyme and cause a low T3 will have the opposite effect on the D2 enzyme in the pituitary gland. 

This means the enzyme will be more active and be able to convert even more T4 into T3 and so the pituitary gland will make less TSH. As a result, your thyroid gland will make less TSH. 

Is this happening to you? 

Let’s take all of this and make it very simple. 

Look at the list of factors that can affect how your D1 and D2 will function in your body. If you suffer with one or more of these factors, then your thyroid tests can look normal to your doctor. 

Your TSH may look normal or even on the low-end. When most doctors see TSH on the low end, they assume you are making too much thyroid hormone. 

Your T4 levels will also look normal or be on the low end of normal (remember that when you make less TSH your thyroid will make less T4). 

Lastly, your T3 levels will be high in the pituitary gland (we cannot measure these levels on blood tests) but will be normal or low-normal on you blood tests. 

In summary your TSH will be “normal” and your T4 will be “normal” and your T3, if it is tested at all will be “normal.” And when I say “normal” this is based on the levels determined by the laboratory that performed the testing. 

You can be in a state of low thyroid function and suffer the effects of low thyroid function and your blood tests will all be “normal.”

Are you taking T4 medication? 

I also want to point that when I am talking about T4 am also talking about thyroid medication. If you take a T4 medication like Synthroid or levothyroxine the same principles apply. Most doctors will use TSH to determine your medication dose. Do you see the problem with this? Any of the factors above can increase the activity of the D2 enzyme in your pituitary gland and your TSH will go down but at the same time you will reduce the D1 enzyme and reduce the T3 in the rest of your body. This is one common reason why doctors are always changing and adjusting medication doses…they are doing what I call “chasing TSH.” 

Many doctors rely too heavily on TSH as the main indicator of overall thyroid function and are not aware of the fact that what the pituitary gland does with thyroid hormone does not necessarily reflect what is happening in the rest of your body. 

This is when the help of a functional medicine doctor can make a huge difference in your health. In functional medicine, we understand that no part of your body works in isolation. Your body can only be healthy, and you can only feel good when the systems of your body work together and in balance. Proper function of your thyroid gland and adequate levels of thyroid hormone are essential for health and wellbeing.

Hashimoto’s Disease 

It’s not what you think it is…

Most of the symptoms you are currently experiencing are NOT due to a problem with your thyroid hormone levels. Much of what you are suffering with is the impact Hashimoto’s has on your brain and the regulation of other hormones in your body. 

This autoimmune disease causes problems in the body far beyond your thyroid gland. The thyroid gland is only one part of the body that is being affected. It causes inflammation in the body, affects the digestive system, nervous system (brain), other hormone systems, disrupts metabolisms and energy production…the list goes on and on. This is why the help of a functional medicine doctor is so important in the treatment of Hashimoto’s disease. Its not just a thyroid problem. Its an immune system disorder and the thyroid is only one its targets.

Hashimoto’s Web of Diseases

Hashimoto’s disease is like a web that touches and entangles other systems in your body. 

Common health issues that occur as a result of this disease include: 

  • Weight gain or inability to lose weight
  • Fatigue 
  • Brain fog / problems concentrating or remembering information
  • Anxiety 
  • Depression
  • Insomnia 
  • Digestion issues 
  • Dizziness 
  • Problems with other hormones (estrogen, progesterone, testosterone, DHEA, etc.) this can lead to PCOS, menstrual cycle problems, scanty or heavy menstruation; infertility, etc.
  • Difficulty regulating blood sugar (high or low blood sugar)
  • Compromised detoxification
  • Cerebellum dysfunction (see picture below) 
  • Autonomic nervous system dysfunction…and can result in dysautonomia. See attached dysautonomia chart.

“There is increasing recognition that the cerebellum contributes to cognitive processing and emotional control in addition to its role in motor coordination. There are also reciprocal connections between the cerebellum and hypothalamus. These pathways facilitate cerebellar incorporation into the distributed neural circuits governing intellect, emotion and autonomic function...”


Hashimoto’s attacks your brain

The same antibodies from your immune system that are causing the damage to your thyroid can also damage your brain. 

How does this happen? 

The one of the antibodies used to diagnose Hashimoto’s is called TPO antibody. This antibody is made by your immune system which causes your immune system to attack and destroy your thyroid gland. 

We now know this same antibody can cause you immune system to attack other parts of your body; in particular, the area of your brain called the cerebellum. Your cerebellum plays vital role in regulation of another part of your brain called the hypothalamus. Your hypothalamus plays a pivotal role in the regulation of your autonomic nervous system and the regulation of not only thyroid hormone production, but many other hormones as well. 

“Initial brain MRI was normal, but follow-up MRI showed diffuse cerebellar atrophy. Similar outcomes have been reported… and anti-TPO antibodies have been shown to bind to cerebellar glial cells.”


Are you experiencing any of the following?

You will notice that I am putting a lot of attention on the nervous system. This is because your nervous system is responsible for the control of so many functions in your body. Again, this is why it is important to consult with a functional medicine doctor if you have Hashimoto’s disease.

Your primary care physician or endocrinologist are not going to do anything for your Hashimoto’s other than prescribe thyroid medication. Getting your thyroid hormones in balance is only the start of managing this complex illness. 

“These connections provide evidence for the key role of the cerebellum and hypothalamus in physiological regulatory processes such as autonomic and endocrine homeostasis.


This means you cerebellum is intimately involved in the regulation of your autonomic nervous system and your endocrine system (the hormone system…estrogen, progesterone, testosterone, cortisol, thyroid, insulin, etc.) This is because your cerebellum affects your hypothalamus…the part of your brain that regulates the autonomic nervous system and the regulation of your hormones. 

Cerebellum, hypothalamus…hormone regulation

Pituitary Gland 

“The pituitary gland is often portrayed as the “master gland” of the body. Such praise is justified in the sense that the anterior and posterior pituitary secrete a battery of hormones that collectively influence all cells and affect virtually all physiologic processes.


The pituitary gland may be king, but the power behind the throne is clearly the hypothalamus. Some of the neurons within the hypothalamus – neurosecretory neurons – secrete hormones that strictly control secretion of hormones from the anterior pituitary. The hypothalamic hormones are referred to as releasing hormones and inhibiting hormones, reflecting their influence on anterior pituitary hormones.”


Your Hormones

We don’t normally think of our brains controlling our hormones, but it that is exactly what is happening. Don’t’ get me wrong, it is more bit more complex than this, but regulation begins in your hypothalamus which then sends directions to your pituitary gland which sends directions to what we call “target glands” like the thyroid gland, ovaries, testicles, etc. 

Summary: Hashimoto’s disease

can have a negative impact on your brain, when this happens it can affect virtually any system in your body. One of the known targets of the brain is the cerebellum. Even subtle compromise of cerebellum function can alter another part of your brain called the hypothalamus. This part of your brain is the origination point of regulation of your autonomic nervous system and your endocrine/hormone system. 

Hashimoto’s disease does more than destroy your thyroid gland, it affects your entire body. 

This is why taking a functional medicine approach is so important. Having your thyroid hormones in balance is just the start…you need to get your immune system in a state of better regulation and protect your brain and the rest of your body.

There are many health imbalances that can lead to thyroid problems. Using a functional medicine approach, we can help you discover WHY you have a thyroid problem and WHAT you can do about it, even when you have been told that your blood tests are “normal” and your thyroid is “working just fine.”

Contact us today and get your health back.**