This is Part 1 of a 3-part series on hypothyroidism and gut health:

Are you allergic to dairy?

OK, that’s a bit of a trick question because if you answered “Yes” then there’s a greater than 99% chance you would be wrong.

A true dairy allergy is very rare.

According to Dr. Raymond Peat…

“In a recent study of 69,796 hospitalized newborns, a diagnosis of cow’s milk allergy was made in 0.21% of them. Among those whose birthweight had been less than a kilogram, 0.35% of them were diagnosed with the milk allergy…

Several surveys have found that of children who have a diagnosed milk allergy, about 2/3 of them grow out of the allergy.”

And given the connection between infant dairy allergy and low birth weight, poor thyroid function is very likely a factor here as well.

But the good news is… you’re not allergic to dairy.

The bad news is… that over the past decade or so, many thyroid sufferers have begun abandoning milk and dairy products over false fears that they are bad for your health.

Now, don’t get me wrong.

Digestive issues and poor milk digestion are in fact common symptoms among thyroid sufferers.

But is dairy the real problem?

Is dairy the cause of your digestive symptoms?

Is dairy the cause of your hypothyroidism?

The short answer to all three is NO.

I’ll get to the long answer in just a minute.

But the important thing to understand is that if you struggle with dairy, then the problem is not the dairy itself…

the real problem is the dysfunction within your digestive tract, which stems from your hypothyroidism.

And when you correct your digestive dysfunction, then you can enjoy dairy and all of the thyroid-supporting benefits that go with it.

Take Linda for example…

After using our approach to thyroid health, she sent me a long personal email, which including this bit:

“How things have changed already. The diet is gentle on my stomach… and I have regained the capacity to drink a lot of milk which I thought I could never do.

Linda S.”

Results like this are not uncommon, especially when you follow the tips that I’m about to share with you.

But first, let’s take a look at how dairy intolerance develops and why you might be struggling with dairy to begin with.

Why Hypothyroidism Sufferers Sometimes Develop Lactose Intolerance

Lactose intolerance occurs for a couple of reasons.

And both are directly related to the bacterial imbalance in your intestines and your inability to produce enzymes needed to digest the milk sugar, lactose.


Research has shown that hypothyroidism itself commonly leads to a condition called small intestinal bacterial overgrowth (SIBO).

Association between hypothyroidism and small intestinal bacterial overgrowth.

“CONCLUSIONS: The history of overt hypothyroidism is associated with bacterial overgrowth development. Excess bacteria could influence clinical gastrointestinal manifestations. Bacterial overgrowth decontamination is associated with improved gastrointestinal symptoms.”

This is a big problem because your small intestine should remain relatively sterile and free of bacteria.

And as mentioned in this study, treatment to eliminate the bacterial overgrowth also resulted in a significant improvement in digestive symptoms including abdominal pain, gas, and bloating.

If SIBO wasn’t bad enough by itself, research also shows that these bacteria create inflammation and reduce enzyme production in the small intestine too.

In fact, these bacteria have been shown to damage the intestinal lining where the lactase enzyme (the enzyme necessary to digest the lactose in milk) is produced.

Effects of an enteric anaerobic bacterial culture supernatant and deoxycholate on intestinal calcium absorption and disaccharidase activity.

“The supernatant decreased the in vitro uptake of calcium by 15% (p less than 0.001). Deoxycholate reduced calcium uptake by 16% (p less than 0.001). Combined culture supernatant and deoxycholate reduced calcium uptake by 39% (p less than 0.001) suggesting a potentiation of supernatant activity by deoxycholate. Culture supernatant and deoxycholate, both alone and combined, significantly reduced lactase, sucrase, and maltase activity. Electron microscopic evidence showed degeneration of microvilli, disruption of mitochondrial structure, and swelling of the endoplasmic reticulum after exposure of the intestinal loops to the supernatant or deoxycholate.”

As you can see, lactose intolerance is a direct result of the effects that hypothyroidism has on your digestive function.

And by fixing your digestive dysfunction, we can effectively reverse your lactose intolerance.

Why Hypothyroidism Sufferers Sometimes Develop Casein (Milk Protein) Intolerance

Casein, a protein found in milk and cheese is also a common cause for debate as many hypothyroidism sufferers are believed to be intolerant to it as well.

However, much like with lactose intolerance, milk and cheese are not the real cause.

As mentioned previously… …the real problem is the dysfunction within your digestive tract, which stems from your hypothyroidism.


It’s well known and research has shown that hypothyroidism leads to both low stomach acid and decreased enzyme production, including the enzyme pepsin.

Effects of thyroid hormones on basal and stimulated gastric acid secretion due to histamine, carbachol and pentagastrin in rats.

“RESULTS: Both basal and histamine, carbachol, pentagastrin stimulated-acid secretion decreased and increased in hypothyroid and hyperthyroid groups compared with control group.”

The real problem is that we require this pepsin enzyme to properly digest the casein protein.

So, in more severe cases of hypothyroidism, the digestion of the casein protein can be inhibited to some degree.

But before you run out and buy digestive enzymes and HCL supplements that are also known to have a number of negative side-effects… there are other safer and more natural solutions.

One such solution is through the use of coffee.

Research has shown that caffeine is a simple and easy way to increase production of both stomach acid and pepsin.

Caffeine-Stimulated Acid and Pepsin Secretion: Dose-Response Studies

“A linear relationship was demonstrated between the plasma caffeine levels and the corresponding gastric acid and pepsin outputs. There was in addition a high correlation between the acid outputs and the corresponding pepsin outputs. It was concluded that both acid and pepsin secretion are stimulated by intravenous caffeine administration, but that acid output is stimulated to a greater degree than pepsin output.”

By using coffee with or after your meals you can very effectively improve your ability to digest both milk and cheese.

In fact, this one reason why many traditional cultures end most of their meals with coffee, such as is customary in France. It very effectively supports digestion.

Coffee and caffeine are also well known to support healthy thyroid function.

In fact, in the 3 Food Triple-Thyroid-Boosting Daily Protocol, I show you a simple way to use coffee to boost your thyroid function and metabolism.


You can download this daily protocol here.

(Note: If you can’t tolerate coffee or caffeine, then this is due to poor blood sugar handling. This is something that needs to be corrected too if you ever want to improve your thyroid health.)

But as with the case of lactose intolerance, casein intolerance is also a direct result of the effects that hypothyroidism has on your digestive function.

And by fixing your digestive dysfunction, we can effectively reverse your casein intolerance too.

With all that being said, there are also many thyroid related benefits that come from including dairy in your diet.

And by missing out on dairy, you’re missing out on these benefits too.

How Dairy Reduces Inflammation, Increases Metabolism, and Improves Thyroid Function

We’ve already established that hypothyroidism and the resulting SIBO are the real cause of lactose intolerance.

But that’s not the only problem…

As mentioned in a previously quoted research study, SIBO can reduce calcium absorption in your small intestine by up to 39%.

And when you don’t get (or can’t absorb) adequate calcium, your parathyroid glands become over-activated and parathyroid hormone (PTH) is overproduced.


PTH is what regulates and maintains blood calcium levels, which it does by removing calcium from your bones to move to your blood stream.

However, as Dr. Raymond Peat points out…

“PTH has many other effects, contributing to inflammation, calcification of soft tissues, and decreased respiratory energy production.”

So, by using dairy for its rich source of calcium, we can effectively help suppress PTH, thus reducing inflammation, while increasing metabolism and energy production… all of which improve thyroid function.

On a side note, this is also important for the prevention of various diseases today, such as the calcification of heart tissue associated with heart disease.

Aside from being rich in calcium, dairy is also rich in…

  • Vitamin A
  • Vitamin B1 (thiamine)
  • Vitamin B2 (Riboflavin)
  • Vitamin B12 (cobalamin)
  • Vitamin D
  • Magnesium
  • Potassium
  • Selenium
  • Zinc

All of which are essential for (and promote) healthy thyroid function and metabolism.

But the benefits don’t end there.

How Casein (Milk Protein) Reduces Stress and Protects Your Adrenal Glands

When you become hypothyroid, your body compensates by over-activating your adrenal glands and stress response.

As it turns out, research shows that the casein protein found in dairy helps to suppress stress hormone production and protect your adrenal glands.

Protection of adrenocortical activity by dietary casein in ether anaesthetized rats.

“The results suggest that high milk protein diet may prevent acute stress effects by protecting adrenocortical activity. The present investigation opens up a new area of management of stress.”

Seeing as how stress hormones directly block thyroid hormone conversion at your liver, casein can effectively help to suppress these stress hormones and improve your thyroid function.

(Note: I cover the importance of liver function with respect to improving your thyroid function in this article on “How to Heal Your Thyroid By Healing Your Liver”)

10 Simple Tips to Overcome Dairy Intolerance

Hopefully by now you’re seeing the recurring theme…

If you have trouble with dairy, then dairy isn’t the problem.

It’s simply a result of your hypothyroidism and the digestive dysfunction that comes with it…

  • The small intestine bacterial imbalance(SIBO)
  • The bacterial induced intestinal inflammation
  • The bacterial induced lactose deficiency
  • The low stomach acid
  • And the decreased pepsin enzyme production

While many will tell you to avoid dairy at all costs… avoiding it won’t help solve your thyroid problems.

In fact, it tends to make them worse in the long run.

If you remember, the many benefits that dairy has to offer…

  • Dairy reduces parathyroid hormone (PTH)
  • Dairy reduces inflammation
  • Dairy increases your metabolism and energy production
  • Dairy suppresses your stress response and protects your adrenals
  • Dairy supports healthy thyroid function

By avoiding dairy, or not getting adequate calcium, not only are you missing out on these benefits, you’re making yourself prone to the opposite effects (inflammation, slow metabolism, and adrenal insufficiency).

So, using dairy to your advantage can make a big difference with your thyroid health.

But what can you do if you still have trouble digesting dairy?

Of course, by regulating thyroid function most if not all of your dairy intolerances will resolve rather quickly and permanently.

But until we get you there, there’s still a lot that we can do to help address your underlying digestive dysfunction so you can tolerate dairy again without problem.

So, here are 10 simple tips that we use with our clients to do just that…

1. Eat one or two raw carrots daily.

Raw carrot has natural anti-bacterial properties helping to reduce the bacterial overgrowth in the small intestine.

By reducing the bacterial overgrowth, we can effectively decrease digestive inflammation and increase lactase enzyme production.

2. Add some honey or maple syrup to your milk.

Adding some sugar to your milk helps to stimulate enzyme production and improves the digestibility of the milk.

This is probably one of the biggest difference makers with my clients. Many who have claimed to not tolerate even the smallest amount of milk find that they no longer have any trouble after this one simple tip.

3. Add some gelatin to your milk.

Gelatin can be used to improve the digestibility of milk by stabilizing the casein protein and improving the digestibility and absorption of the milk fat.

4. Use Thyroid Hormone (T3).

Using thyroid hormone directly improves enzyme production, reduces bacterial overgrowth, and re-energizes your digestive tract, all of which improve dairy tolerance significantly.

5. Address Your Progesterone Deficiency.

Hypothyroidism is well known to cause estrogen dominance and progesterone deficiency.

And according to Dr. Raymond Peat progesterone deficiency is directly associated with lactose deficiency.

6. Increase milk consumption slowly.

Your enzyme production depends largely on the foods you eat regularly.

So, if you’ve avoided dairy and/or milk for a long time, then your body won’t actively produce large amounts of the enzymes needed to digest it.

Start with as little as a tablespoon of milk with each meal and increase it slowly over time.

Research has shown that increasing milk consumption itself improves lactose intolerance.

7. Try different variations of milk to find what works best for you.

According to Dr. Raymond Peat, oftentimes allergies to milk have more to do with the feed used with the cows.

This is why we recommend that our clients try different brands or sources of milk to find which works best for them.

What we found is this…

Some do best with raw milk, while others can’t tolerate the higher levels of bacteria.

Some do best with reduced fat milk as opposed to whole. Oftentimes allergens from the cow’s feed are stored in the milk fat. So, reducing the milk fat exposes you to fewer allergens.

It’s always best to let your taste guide you as most people tend to do best with milk that tastes the best to them.

It can take some experimentation but it works wonders when you find the right source for you.

8. Use Coffee.

As mentioned, coffee and caffeine used with or after a meal can significantly help improve casein digestion and tolerance.

9 Avoid cheeses with microbial and GMO rennet.

Traditionally, cheese was always been made using rennet enzymes from animals.

Today, more and more cheeses are being made with cheaper rennet substitutes derived from mold which can be very problematic and irritating to the digestive tract.

These days, this poor reaction to mold derived rennet is oftentimes falsely mistaken as casein intolerance.

The safest cheeses are those which are still required to be made using traditional animal rennet, such as Parmesan.

10. If all else fails, use calcium carbonate.

In the event that dairy cannot be used due to fear or rare case of extreme allergy, we can use an alternative source of calcium initially while digestion improves. And then re-introduce dairy at a later date.

However, calcium must be properly balanced, so the best sources are powdered calcium carbonate which can be obtained from eggshells or oyster shells.

So, there you have it…

With so much negative publicity surrounding dairy today, maybe you’ve been avoiding it out fear.

Or maybe you are sensitive to dairy right now.

The truth is that dairy isn’t the problem and avoiding dairy sure isn’t the solution.

By fixing the underlying digestive function and using the tips I just gave you, you can get all of the benefits that dairy has to offer…

…including its ability to help improve your thyroid health.

So, tell me.

Are you a fan of dairy?

Or are you afraid?

Let me know in the comment section below.