How to Overcome Dairy Intolerance Once and For All

By |2019-07-18T19:19:18-07:00January 21st, 2016|Hypothyroidism, Nutrition|88 Comments

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.

About the Author:

Tom Brimeyer is the founder of Forefront Health and the creator of the popular Hypothyroidism Revolution program series. Specializing in thyroid and metabolism disorders, Tom's work has impacted over 50,000 people spanning more than 60 countries. Tom is also a highly sought after practitioner who runs a successful health consulting practice where he continues to help clients across the globe to take back control of their lives from their devastating health conditions.


  1. Lynn January 21, 2016 at 6:41 am - Reply

    Would you please tell me how to access your health consulting practice?
    Thank you.

  2. Jocelyn January 21, 2016 at 7:19 am - Reply

    Hi Tom, from what I understand about caseine is not that it is an allergic or maldigestive issue, but that it causes the same auto immune reaction as gluten as it looks like thryoid tissue. What is your idea on that?

    • Tom Brimeyer January 21, 2016 at 11:08 am - Reply

      Hi Jocelyn, there is some research that suggests that the use of cow’s milk too early (within the first few weeks of life) can increase risk of type 1 diabetes in childhood but that’s about it. There is no evidence of increased immune/autoimmune reaction with respect to casein and Hashinmoto’s thyroiditis.

  3. Margaret January 21, 2016 at 10:24 am - Reply

    Hi Tom: Great article. Personally, I do fine with raw milk. I got that in Tucson, AZ, at a health food store, but I can’t get it in this area of Texas. Also, no problems with goat milk, the one that can be purchased at the grocery. However, it is very expensive.

  4. Cindy Huff January 21, 2016 at 10:29 am - Reply

    Thanks, Tom – great info! When I resorted to giving up dairy for nearly 2 years, trying to figure out what was going on & wanting to try eliminating all the known potential “hot spots”, (dairy was the last one I tried, BTW, ‘cuz both my parents were raised on farms & there are still working farms in the fam on both sides, and both my parents are super healthy, so I waited on that one & now wish I hadn’t tried that, but wasn’t finding any real helpful info like this post you just posted!), the only things I got in return were low VitD levels for the first time in my 47 years of livin’ life and low energy. I am happy to see clearly part of what was going on when I did that. Thank you & thank the good Lord, I’ve since gone back to dairy & loving it & all the benefits! 🙂

  5. Dawn January 21, 2016 at 12:00 pm - Reply

    I seem to digest dairy just fine, but 2 days later, it gives me painful, scarring cystic acne and eczema flare ups, also signs of a leaky gut. If you have acne, it is recommended you quit dairy because of the hormones in it.

    Will correcting hypothyroid help with this kind of dairy intolerance?

    • Tom Brimeyer January 21, 2016 at 12:15 pm - Reply

      Hi Dawn, milk does have hormones and does naturally promote increased hormone production. But when you get cystic acne, that’s a sign of underlying hormonal issues that need to be corrected. It’s still not the dairy that’s “causing” the issue. Because we have to correct these hormones in order to regulate thyroid function, it would in fact help.

  6. Lianda January 21, 2016 at 12:16 pm - Reply

    Can you write about what causes fatty liver-? Is it caused by sugar (as in soda-pop), as Dr. Mark Hyman says?

    and also, you write about Hypothyroid- how different are these issues when someone has Hashimoto’s Thyroiditis, but symptoms of both hypo and hyper from time to time?

    • Tom Brimeyer January 21, 2016 at 3:02 pm - Reply

      Hi Lianda, there’s one single cause to fatty liver although we don’t recommend the use of HFCS, which can contribute, there’s much more involved. With Hashimoto’s or even hypothyroidism in general one can experience “hyper” like symptoms because adrenaline can rise quite high. It’s the adrenaline that is causing the symptoms. With Hashimoto’s, when the gland becomes blocked due to the effects of estrogen, thyroid hormone can build up and then unload too much thyroid hormone. Too much thyroid hormone will make your more sensitive to adrenaline, amplifying the effects. With Hashimoto’s this can become cyclical and is oftentimes referred to as a “thyroid storm”

  7. Gwenda January 21, 2016 at 1:49 pm - Reply

    Great article. I thought I was just ‘lactose intolerant’ ( which has grown worse over the years ) but find that even lactose-free milk gives me problems so decided that it was the casein as well, (also sensitive to wheat/gluten). I have borderline osteopenia in some parts of my body so the calcium deficiency is showing up. Some GPs seem to know that hypothyroidism and osteopenia are linked which is why when I broke my toe she wanted it checked. And sure enough another offshoot symptom of hypothyroidism appears.
    Though the outlook for hypothyroidism seems bleak,your research is pretty spot on.

  8. Beth January 21, 2016 at 2:17 pm - Reply

    Hi Tom, After I cut out gluten and dairy from my diet, my TSH went from 8, down to 3.2, and my antibodies back to normal. I am not on any medications. I then decided to add in some dairy again (yoghurt), and after a few months, my TSH went up to 4.6. Unfortunately I didn’t check the antibodies. I would like to try the coffee, but I hate the taste … does it come in tablet form? Thanks for the great information!

    • Tom Brimeyer January 21, 2016 at 2:25 pm - Reply

      Hi Beth, keep in mind that TSH is suppressed by stress as well which is one of many reasons it should never be used as a direct indicator of thyroid status. Also, yogurt wouldn’t be recommended as that alone could contribute to the problem. The higher lactic acid can burden the liver and therefore suppress thyroid function at the liver. Gluten itself is a different story and should be avoided although it’s an issue related to estrogen dominance.

  9. Judy January 21, 2016 at 2:50 pm - Reply

    Hi Tom how do you obtain T3 I would like to get some can you suggest some one or company and how much to use.

    • Tom Brimeyer January 21, 2016 at 2:53 pm - Reply

      Hi Judy, this is something that we’re currently working on putting together.

  10. Shakeh January 21, 2016 at 3:32 pm - Reply

    Hi Tom, I am hypo for long time on armour thyroid, using digestive enzym and HCL to digest the food. Not using any dairy for months. It is very interesting that you say hypo people have SIBO. I have done SIBO test and it is negative. The reason doing SIBO test was because of the bad breath I am experiencing. That is the reason stopped using dairy but it did not help. If there is SIBO present, can that cause bad breath? Can H. Pylori cause that?
    Anyone has this problem? I would like to hear if you have the same situation.
    Thank you for your time and help.

  11. Leisa Douglas January 21, 2016 at 5:58 pm - Reply

    Hi Tom,
    I couldn’t believe my eyes when I read this article – thanks!
    I was told to go off dairy when diagnosed with Hashimoto’s. Several years later, I developed an overactive parathyroid gland, which had to be removed. I CAN NOW SEE WHY. I now have an IgA response to dairy proteins, sugar and fat, with a large weight gain tomorrow if I eat dairy today (usually 1kg or more) and abdominal symptoms. I want to get back on to dairy, and now I am armed to give it my best shot. THANK YOU Tom, for showing me why, and helping me avoid developing more parathyroid issues.

  12. Rachelle January 21, 2016 at 7:46 pm - Reply

    Hi Tom! I was diagnosed with Hashi’s 3 years ago and have been off gluten and all dairy for 3 years. Was told I am gluten and casein intolerant. I have worked so hard on my gut that I am scared to try dairy again. I still struggle with adrenal issues, but my gut has improved greatly. Thyroid symptoms include some mild brain fog, cold hands/feet and mild depression. If I was to introduce dairy again, what kinds of dairy, specifically, would you suggest consuming. Fear stricken to undo the good I’ve worked so hard to achieve…. Thanks

    • Tom Brimeyer January 21, 2016 at 8:11 pm - Reply

      Hi Rachelle, the biggest problem for most is the unwarranted fear. But one point I try to emphasize with clients is that trying to solve one problem only to create another is never a true solution. But if you’ve avoided dairy for 3 years then you’ll need to start very slowly. Most reintroduce the wrong king too quickly. Or as I mention in the article, start with the calcium carbonate so that you can begin to correct the underlying problem. Plenty of suggestions are provided in the article.

  13. Kim January 21, 2016 at 10:04 pm - Reply

    Thanks for this article! It explains “me” very well. Do I still need to reintroduce dairy slowly if I have been using lactose free milk? Also, I haven’t used milk for the purpose of just drinking it in probably 30 years. Even as a kid I didn’t like the taste of it. Could I get away with using chocolate milk?

    • Tom Brimeyer January 21, 2016 at 10:10 pm - Reply

      Hi Kim, If you’re going to use a milk that contains lactose then yes, very slowly. Try some different brands/sources and see if one tastes better than the others. As for chocolate milk, store bough should be avoided as it almost always contains carrageenan, gums, or other thickening agents that are very irritating to the digest tract. Homemade chocolate milk without any of of the bad stuff can work great.

  14. Shelley January 21, 2016 at 10:12 pm - Reply

    Very informative article Tom, thanks much for the work you do! I love dairy, but for most of my life when I eat more than a little my ears get very watery, and sometimes itchy, it’s weird! If I eat quite a bit of it on a regular basis my head gets really stuffed up. I don’t noticeably have any of the other issues you mentioned. Do you have any idea what this could be from? Oh, and I’m hypothyroid, have adrenal issues, trying to figure it all out!

    • Tom Brimeyer January 21, 2016 at 10:19 pm - Reply

      Hi Shelley, dairy will increase mucous production which is not a bad thing. Our mucous membrane is our primary immune defense barrier that protects our insides from the outside world. With that being said… hypothyroidism itself creates a lot of inflammation and tissue swelling. So if the sinuses are already inflamed then even a slight increase in mucous production can further impinge the sinus passageways. Oftentimes bag breathing and retaining carbon dioxide is enough to temporarily reduce inflammation and open the passages. However, it’s not a long term fix. The long term fix is to regulate thyroid function to prevent carbon dioxide loss and decrease the underlying inflammation.

      • Shelley January 21, 2016 at 10:24 pm - Reply

        Thanks! And carbon dioxide loss is something more to be aware of and learn about!

  15. Sharene January 28, 2016 at 12:57 am - Reply

    Hi Tom, thanks for the info! The first I’ve read on that perspective, which gives me hope for myself and my two young children! Just wondering though, how it might apply to me – my mother went off dairy and wheat while breastfeeding me (and my twin) because we both developed thrush in our mouths. It went away following that. So I’ve obviously had ‘milk allergies’ since a baby (and my toddler and baby also seem to ‘do better’ on a dairy-free diet). Does that mean I had thyroid issues from birth? (I’ve had digestive issues all my life, fatigue issues for almost as long and only now starting to see it’s probably not the gut exclusively, or adrenals, but thyroid. Also have very poor methylation on a cellular level according to genetic testing). What would you recommend for young children?

    • Tom Brimeyer January 28, 2016 at 10:05 am - Reply

      Hi Sharene, this was mentioned in the article “Several surveys have found that of children who have a diagnosed milk allergy, about 2/3 of them grow out of the allergy.” So, a true allergy is rare even among infants but even those who are allergic, most do grow out of it. The need for calcium in children is very important as they have a very high metabolic rate and grow rapidly.

      • Sharene February 4, 2016 at 5:30 am - Reply

        That’s great for the 2/3! 🙂 Unfortunately it sounds like I’ll always have a sensitivity to dairy. Does it ‘pass down’ to children then? Apart from butter and cheese, my boys have had very little dairy in their diet. How will I know if they have a ‘true allergy’? (For me, for example, I develop a sore throat immediately after eating yoghurt. Mucous congestion from eating more dairy than usual).

        • Tom Brimeyer February 4, 2016 at 1:33 pm - Reply

          The mucus production is typically a result from something in the dairy irritating the intestines. Trying different types and brands can help.

  16. Bernadette January 28, 2016 at 11:08 pm - Reply

    Hi Tom! Facinating information you have to share. I’ve been hypo for a long time, I battle extreme fatigue all day, but drinking coffee helps a ton. I always thought I was doing more harm with drinking coffee. This info makes me feel happy it doesn’t. I have been taking armour thyroid for about 12 years, on the same dose. Interestingly while pregnant my dose needs to be slightly less or I get high blood pressure… Strange because I weigh more, wouldn’t I need more thyroid?
    Anyway, I have been what I thought milk intolerant forever as I’ve avoided it because it gives me a lot of mucus in my throat. My 3 year old was born with a lot of allergies, (nut, soy, seed, wheat, milk?) now I feel like he has had leaky gut the whole time! He would get very flemmy drinking milk though. Why can we eat cheese with no problems? So weird. We have avoided milk but I don’t want to cause problems later. I’ve had three kids in a row, we have a 1,2 and 3 year old. We eat a whole food diet, with lots of veggies, but maybe they need milk!
    Also, I took a 24 urine test and all of my hormones are very low; progesterone, testosterone, estrogen, dhea, cortisol and other hormones. I find it very interesting the link with progesterone and lactose deficiency! I feel like since I had my daughter 1 year ago, my thyroid and adrenals have been so taxed and have had a hard time regulating, getting back to normal. I am trying to find natural ways to help support my body and it gets very confusing when the thyroid is in the mix. Like what to work on first. I am gluten free and that’s helping…but I’ve heard carrots would help rebalance me, would milk help to if I introduce like you say in the article? Thank you!

  17. Lola Tobiasson March 22, 2016 at 7:22 am - Reply

    Wow -this info is really awesome and somehow in the back of my mind it does makes sence. Born in the early seventies and now mild hypo without meds I can see why my parents insisted on us drinking milk and even allowing us coffee as young children – stopped drinking milk years ago to “slim down” getting leaner. I loved drinking milk specially with a bun of bread. Well, i’ll leave the bread out now.
    So now that milkproducts are fine to consume, what about high fat youghurts like fullfat greek youghurts?
    Are all youghurts OK as long as they are sugarfree? Or are we to consume milk and cheese only?
    Great article, thanks a lot from the Netherlands/ Lola

    • Tom Brimeyer March 22, 2016 at 8:28 am - Reply

      Hi Lola, greek/strained yogurt it OK because most of the lactic acid is removed through the straining. I don’t recommend other yogurts as the lactic acid content from the fermentation is a significant burden to your liver. Keep in mind that fermentation of foods was really used as a means of preservation before modern day refrigeration. It wasn’t used to make foods superior to its original form as many people are led to believe today.

  18. Anthony Llabres March 24, 2016 at 6:57 am - Reply

    Outstanding article Tom!!!

  19. Kandy Thompson March 24, 2016 at 5:24 pm - Reply

    Any type of milk I drink I get alot of mucous and phlegm which makes me cough quite a bit. I need to know how to specifically correct this problem.

    • Tom Brimeyer March 25, 2016 at 9:50 am - Reply

      That’s commonly caused by a sensitivity to an additive used with the milk or a sensitivity to something used in the cow feed.

  20. Beth March 24, 2016 at 6:32 pm - Reply


    I have recently been making milk kefir, hoping it will help with my gut-issues. You mentioned above that yogurt wasn’t as good as milk. I assume that would refer to m kefir as well?? Also have been making kombucha for the probiotics.. What is your take on this? I have really been enjoying these added foods.

    I’m currently in an RV for the rest of the season, but when we get home, plan to start your program.

    Thanks for all the info, I’m slowly ‘digesting’ it!

    • Tom Brimeyer March 25, 2016 at 9:51 am - Reply

      Hi Beth, yes kefir also contains large amounts of lactic acid, which is a burden to the liver.

  21. Abby March 25, 2016 at 8:48 am - Reply

    Hi Tom, thanks for the interesting and thought provoking article. I have cut out milk for probably 3-4 years. I do have hypothyroidism more subclinical and support the thyroid with a lot of the vitamins and nutrients you mentioned above. My naturopath did a blood test which shows an allergy to cow’s milk with positive IgE. My symptoms never seem to be digestion so much as respiratory with a lot of mucous production, i.e. post nasal drip and quite soon after I consume dairy products. Any thoughts on that?

    • Tom Brimeyer March 25, 2016 at 9:53 am - Reply

      IgE allergies tend to be more severe so you have to be much more careful. The mucous production is a common sign that the sensitivity is to an additive in the milk or to something used in the cow feed.

  22. Bob April 11, 2016 at 5:40 pm - Reply

    There is research suggesting that milking pregnant cows delivers milk high in estrogen.

    • Tom Brimeyer April 11, 2016 at 5:51 pm - Reply

      Hi Bob, if estrogen were too high it would interfere with the lactation of the cow and it wouldn’t be able to produce milk. With that being said, the estrogen in milk isn’t very high and it’s pre-packaged in a way that it is easily detoxified. But more importantly, the amount progesterone in milk is more than enough to offset it. If you’re still concerned, then you can use lower fat milk as the estrogen accumulates in the milk fat.

  23. Juliette April 28, 2016 at 2:12 pm - Reply

    Hi Tom,

    I have 2 questions for you. I have completely eliminated dairy finally in my diet, for about 7 months, and have finally been able to lose weight. I no longer get acne anymore either. My questions are these:
    1. If I reintroduce dairy into my diet and fix any overgrowth of bacteria, will I still gain weight, or was the weight gain caused by the inability to digest dairy (rather than the dairy itself)?
    2. And the same question goes to acne – will the reintroduction cause an onset of acne again (from what I understand acne from dairy is caused by IGF-1 protein)?

    Thank you very much, and excellent site and articles!

    – Juliette

    • Tom Brimeyer April 28, 2016 at 4:49 pm - Reply

      Hi Juliette, acne can be caused by a number of factors but most commonly a vitamin A deficiency and/or excess estrogen/prolactin. Since dairy increases hormone production is can make both imbalanced more pronounced. Cutting out dairy and lowering thyroid function and hormone production can show improvements in acne but it’s not necessarily a healthy solution.

  24. ELAINE April 28, 2016 at 3:25 pm - Reply

    Tom. This article is really good news. I have been diagnosed with Hashimotos disease for over 20 years and have been lactose intolerant for about 15. I now use goats milk and goats cheese and goats butter instead of any dairy products. I am very nervous to try any dairy due to terrible stomach pains, swollen fingers, headaches, mucous etc that dairy products cause in me. Are you saying that goats products can not be used as replacement? I was on 200 microgrammes of levothyroxine for many years and was coping well but new gp has reduced me to 175 and now 150. I have mild depression, huge cold issues, terrible brain fog, weight gain, hair loss and no energy. I am putting myself back on 200 microgrammes to get myself up and running again but also because of gp concerns that overdosing could cause heart issues I am trying to research more in to getting myself better hence I found your site. However I have found other sites that tell me to give up coffee and gluten. I am confused as to why there is conflicting advice? I love my coffee! I am based in UK.

    • Tom Brimeyer April 28, 2016 at 4:27 pm - Reply

      Hi Elaine, goats milk is perfectly fine to use. As for coffee you’ll find that low-carb advocates don’t recommend it because their dieting depletes the liver of glycogen, is unsafe, and will cause a negative response. So, the problem isn’t the coffee but rather the poor dieting.

  25. Kerry May 11, 2016 at 8:35 pm - Reply

    Hi Tom! I find this article very interesting especially since it’s the first article I’ve read that actually suggests a correlation between leaky gut and hyperparathyroidism. I’ve suffered with persistent hyperparathyroidism since 2001 and have had 2 glands removed. I have 2 remaining but no surgeon can find these to be enlarged after 2 years of nuclear imaging. Coincidentally, during my last scan, the surgeon disclosed that no adenine was found but my thyroid appears as though I have Hashimoto’s. Sure enough, my antibodies were in the 900s and my FT4 was very low. Fast forward to the present and I’m seeing a functional med doc to help me heal my leaky gut (have had gut issues my entire life). Also have candida issues. My question for you is…although SIBO prevents the intestines from absorbing calcium thus causing an increase in PTH, would it also cause hypercalcemia? I ask because not only is my PTH elevated but my calcium has been high since 2001. Would it make sense that since the intestines aren’t absorbing the calcium, it would just end up in my bloodstream causing the elevated levels? Thank you!

    • Tom Brimeyer May 13, 2016 at 12:17 pm - Reply

      Hi Kerry, that’s what the parathyroid glands do is regulate blood calcium. So if PTH is elevated, which it can be for a number of reasons, then your blood calcium will be high. Not because your absorbing it through the intestines but because it’s being leeched from your bones.

  26. Veronika Worr May 15, 2016 at 5:50 pm - Reply

    Hi. Thank you so much for all the information you are providing. I was fine with dairy when we lived in Europe until age 15. We lived in the country and Frank local unpasteurized milk. At age 15 we moved to Canada and shortly thereafter at age 17, I started getting severe stomach pains and major debilitating migraines whenever I consumed dairy. It took me several years to figure out it was related to dairy. I then cut out dairy completely for a few years and reintroduced it slowly. I am 33 and to this date I cannot consume too much dairy as my migraine headaches and stomach pains return. I read the comments and most people are indicating their side effects are mucous and sinus related; I personally do not suffer from this. Because of the pain and vomiting associated with migraines, I am very fearful of reintroducing dairy to this degree (Currently I can eat cheese and plain Balkan yoghurt in reasonable amounts a couple of times per week without symptoms). Do you know what could be causing my stomach pains and migraines in the dairy? Or is my reaction related to something else? Thank you 😉

    • Tom Brimeyer May 19, 2016 at 9:17 pm - Reply

      Hi Veronika, as mentioned, lactose intolerance is common with hypothyroidism so everything in the article provided would apply.

  27. Veronika Worr May 15, 2016 at 5:54 pm - Reply

    Oh and I forgot to mention: I’m hypothyroid and am currently taking 75mg of Synthroid. My last test indicated that I lowered my numbers from 5.5 to 2.
    I have candida issues and digestive issues and have been for 20 years. I am just now finding out how it is all connected. It took me almost 1 year of research and a bit of luck to figure this out. I am now working on correcting it. I have cut out gluten and I have limited sugar consumption to fruit only. Thank you.

  28. Kirstin May 22, 2016 at 6:32 pm - Reply

    Hi Tom, I do not have hypothryoidism or SIBO, but have issues with tolerating milk, which on,y started about 5 years ago and I also have leaky gut. I cannot add sugar or honey to milk due to having insulin resistance. I am also in Perimenopause and wonder if that could be contributing to the milk issue? Milk also give me bad mucus issues. Thanks.


    • Tom Brimeyer May 23, 2016 at 1:18 pm - Reply

      Hi Kristin, I wouldn’t assume you don’t have hypothyroidism or SIBO. I would recommend using our testing to protocol to determine that here:

      Perimenopause involves a number of hormonal changes that can cause and/or worsen hypothyroidism, i.e. progesterone deficiency which is directly related to lactose intolerance.

      As for insulin resistance and diabetes, it’s not a sugar problem or worsened by sugar as covered in detail here:

      • Tom Brimeyer May 23, 2016 at 1:19 pm - Reply

        Also should have mentioned that anyone who is diabetic or severely insulin resistant will also be functionally hypothyroid because of it.

  29. Kirstin May 25, 2016 at 3:50 pm - Reply

    Thanks, makes sense.

  30. Barbara June 6, 2016 at 6:03 pm - Reply

    Wow, I am going to have to read this again, so much to learn. I had the blood allergy test done where I got the info regarding gluten, Lactose, casein & other intolerances. This was about late 1990s, but I see the pattern & wonder if taking care of the leaky gut will overcome or fix Thyroid? I haven’t gone through the whole program as yet. The Bone Broth, DGL, etc., does seem to be helping.
    God bless you for all the help.

  31. Bob June 9, 2016 at 12:23 pm - Reply

    So in conclusion, it seems that most people with hypothyroid issues also have lactose intolerance, yet we should consume dairy to help the thyroid, but not yogurt or kefir which have the healthy bacteria to heal the gut. This seems sort of contradictory.

    One could take enzyme supplements with the dairy, or use goats milk and cheese.

    What about organic and gmo-free cheese or grass-fed?
    What about the BPA chemical in all the food and drink packaging for the dairy- which accelerates estrogen dominance?

    Thanks- great information, just trying to synthesize it will all the other info.

    • Tom Brimeyer June 9, 2016 at 12:32 pm - Reply

      Lacto-fermentation produces lactic acid, which is a burden to the liver. Hypothyroid people already have high levels lactate due to low carbon dioxide and dysfunctional metabolism. Burdening the liver even further is never a good idea. Restoring liver function, which we focus on, protects against estrogens.

  32. Christine June 17, 2016 at 6:29 pm - Reply

    Thank you for the info, being rather isolated here in Tasmania Australia, your emails/links have helped me perceive the fog parting & therefore understanding gradually that there is light at the end of the tunnel.
    Fond Regards,

    • Tom Brimeyer June 19, 2016 at 7:14 am - Reply

      Hi Christine, that’s great to hear and thanks for sharing.

  33. Donna June 17, 2016 at 11:14 pm - Reply

    Thanks Tom. I grew up on a grass fed dairy farm drinking milk warm from the cow. It was great. The rule was, we weren’t allowed to pour a glass without stirring it, otherwise there was just skim milk left (yuk!) I generally handle dairy well except it tends to make me feel sluggish first thing in the morning and if I eat hard cheese (pizza/Mexican) my weight is always up the next day.

  34. Linda J. June 18, 2016 at 11:59 pm - Reply

    I have issues with digestion… tried HCL, but it didn’t agree with me, It seemed strong. I’d love to try the coffee, but i”m very sensitive to caffeine. I need to drink it before noon or I can’t sleep. Would de-caf work for lunch and dinner?

    • Tom Brimeyer June 19, 2016 at 7:12 am - Reply

      Yes, that can still be beneficial, but using caffeinated when possible is best.

  35. Nancy July 18, 2016 at 3:09 pm - Reply

    Hi Tom, thank you for the very helpful information! I’m wondering about 2 things: First question…
    I’m hypothyroid and anemic right now (ferritin is quite low). I have read that caffeine should be avoided for 2 hours prior to a meal and 2 hours after a meal to improve iron absorption rates. How can I consume caffeine without jeopardizing iron absorption?
    The other question is about dairy – I’ve read that dairy is very acidifying to the body and is linked to osteoporosis (stealing calcium from the bones to stabilize pH levels..). Do you have a different way to look at this? Also dairy is linked to eczema/skin issues, but perhaps that has something to do with absorption problems in the gut (…and the thyroid…). Thank you for any insights you can share.

  36. Nancy July 20, 2016 at 2:09 pm - Reply

    Hi Tom, thank you for your reply. I am interested in the Truth so I explore new information whenever I can. I’ll check out your links. My understanding of ferritin is that it stores iron, so if ferritin is low, then a person is very likely anemic. If this is not true, can you share another way to look at it? For the purposes of brevity, I didn’t not mention in my previous post that a number of components of my previous cbc’s/differential results were low: Hematocrit, Hemoglobin, Mean corpuscular volume, Mean corpuscular hemoglobin as well as lymphocytes. I am in study mode about how to correct this – I think it starts with the thyroid (and getting enough iron in my diet). I’ve stopped taking the 300 mg/day of iron because I was feeling sick from it. Feeling better now. Just hungry to help heal my thyroid and iron levels. Thanks very much for the helpful information.

  37. Bob July 29, 2016 at 11:02 am - Reply

    Hi Tom,

    What do you think of goitrogens?


  38. nadine August 21, 2016 at 4:50 am - Reply

    Hi Tom,
    i feel a little bad because I went to 2 doctors and they wanted to test my thyroid.As my mother had some surgery in this area I felt by all cost I don’t want any test.By a wonder I came into your articles etc. I follow your diet now for 4 days, even I have no doctor diagnose I know my thyroid and age, stress is out of range. I am diagnoses with dairy sensitivity I cut out the dairy just a little every 3 days. The problem is I am quiet thin cannot gain weight easily. In fact with dairy I can. So I am feeling much better already. Got full back on milk, cottage cheese etc.The only thing was I got a strong headache for 2 days which I had already before sometimes. I suffer in general from anxiety and panic attacks. I am so glad reintroducing all the food I once loved and before society tried to make you feel bad about coffee, milk, meat etc. You are a gift and a provider for right information also to help people clear their confusion is especially meaningful in this times.

  39. Bob September 10, 2016 at 12:55 pm - Reply

    This doctor says to avoid fructose in fruits if one has liver issues:

    • Tom Brimeyer September 12, 2016 at 1:29 pm - Reply

      Hi Bob, research shows that fatty liver as a result of sucrose consumption has very protective effects against lipid peroxidation, which is the primary concern with fatty liver:

      Studies have shown that adequate high quality protein can completely prevent and reverse it, indepdent of carbohydrate and fat intake:

      If you haven’t it’s also worth getting your vitamin D checked which most doctors will do. Vitamin D deficiency will increase risk of fatty liver.

  40. Karin Le Roux September 16, 2016 at 11:35 am - Reply

    What am I to do when I have symptoms like SIBO? I get bloated if I eat fruit/veggies.

    • Tom Brimeyer September 19, 2016 at 8:42 am - Reply

      Hi Karin, we do many things to improve SIBO in the HR Program. But a high fiber diet tends to worsen it. Of course, improving thyroid function is key to keeping the bacteria out of the small intestine and where they belong.

  41. Charlotte Tessore September 17, 2016 at 2:57 pm - Reply

    Trying your diet, 3rd day. Using goat milk for the liquid milk. Lungs feel full again, and my ears hurt, but my throat hasn’t felt like its closing up yet. will keep going. Have been surprised at my blood sugar numbers, not bad.

    • Tom Brimeyer September 19, 2016 at 8:40 am - Reply

      Hi Charlotte, if you have severe reactions to dairy, then as mentioned, using the eggshell calcium can be a life-saver until the inflammation and digestive dysfunction are resolved.

  42. Suzanna September 20, 2016 at 10:07 pm - Reply

    Hi Tom,
    I have read many of your articles by now actually write down the info to really understand and incorporate it to my life. How come our gp’s don’t know this stuff? I have been diagnosed nearly 14 years ago as Hypothyroid but first 7 years ago the diagnosis of Hashimoto’s. And all the above you mentioned I did…cut out dairy because I had increasing problems with digesting….never been told to go gluten free etc etc, so being in a spiral of complications due to cutting out the dairy. I’m on levothyroxine and take HRT, since my menopausal symptoms were so bad…and this is since 6 years. Happy to continue to learn. I did a liver cleans but understand, that there are still enormous many factors I have to correct to get to better health. Maybe 7/8 years ago I used progesterone cream to help my menopausal symptoms. Is this something I should try again for a shorter period to help to balance my estrogen?
    Thanks for all you articles and help you have been so far to me and so many others.

    • Tom Brimeyer September 29, 2016 at 2:36 pm - Reply

      Hi Suzanna, unfortunately the medical system has one approach only, medicate with inappropriate thyroid medication. Until the standard medical treatment changes, doctors just follow the rules.

  43. Christina September 23, 2016 at 1:44 am - Reply

    Hi Tom,

    Just started your 7 day meal program. Feeling so much better! I was using 24 hour yogurt I make at home instead of the cottage cheese. Would straining it be okay or is it best to leave it out?

    Would love to get your thoughts on probiotics? I currently take acidophilus, bulgaricus, and bifidum (Natren Brand).


    • Tom Brimeyer September 29, 2016 at 2:08 pm - Reply

      Hi Christina, just sent you an email.

  44. Kate November 11, 2016 at 1:41 am - Reply

    I don’t really understand the need for dairy. All the benefits listed in this article (high in calcium, vitamins, minerals, etc) can all be obtained from eating the same leafy greens the cow ate. Can’t we achieve the same (if not better) results if we choose not to eat dairy?

    • Tom Brimeyer November 14, 2016 at 2:40 pm - Reply

      Hi Kate, plant leaves contain plant toxins (some are anti-thyroid), which is one primary reason we don’t use them as viable source of calcium. And we get a lot more than calcium from dairy products that you can’t get from plants.

  45. Kimberly Repscha November 14, 2016 at 1:32 pm - Reply

    Hi Tom, I’m starting the diet today. I have Hashimotos. I was started on Levoxly and now a T3 med alone with it and I’m on HRT because my hot flashes were so bad that I didn’t sleep for a year. I am weaning off the estrogen after reading other articles you’ve written and just going to use the progesterone. YAY!
    I have been off dairy for 2 yrs after IgE allergy tests showed I was allergic to cow’s milk but not goat but your article makes sense to me, so I’ll work it slowly back into my diet. However I also show being VERY allergic to eggs! I’ve had sinus infections most of my life and used antibiotics and steroids to clear them up, It’s been 2 yrs since I’ve had one and I’m worried about eating them again. What can I substitute for them and do you have any thoughts on egg allergies being linked to Hashimotos?

    • Tom Brimeyer November 14, 2016 at 2:47 pm - Reply

      Hi Kimberly, if you do well with goat’s milk then there’s no need to change what’s working. As for eggs, there are some other options, so feel free to contact support for more help.

  46. Kimberly Repscha November 18, 2016 at 7:11 am - Reply

    Hi Tom, I’ve been drinking Bullet Coffee for the last year. What are your thoughts on that given that it adds butter and coconut oil to the coffee.

    • Tom Brimeyer December 2, 2016 at 1:03 pm - Reply

      Hi Kimberly, it’s not something I recommend.

  47. Nannette Lancaster February 20, 2018 at 7:56 am - Reply

    Wow, Tom reading all these post is like seeing my life pass before me! so many commonalities in health issues, all ones I have experienced. As I feel all my symptoms are getting worse after dealing with hypothyroid, Hashimoto,parathyroid tumor, lactose intolerance, among other things which now may include other conditions caused by years and years of not enough information. I hope to start your program and I can call to order your products. It will be a lot cheaper than lets say the MRI I am getting this week due to probably mal absorption of nutrients like dizziness, loss of balance, brain fog, tingling, numbness. Thank you and Lord Bless you Nannette

  48. S Edwards January 3, 2019 at 9:39 am - Reply

    Hi, I found this info fascinating and pertinent for me.
    I recently changed to using A2 milk which is avail in the U. K. It is milk from breeds other than the typical dairy cows. My stomach has settled completely. So it is worth trying different brands.
    Also I started eating a little cheese just before bed along with my usual diphenhydramine tablet. The result has amazed me as I have stopped waking at 4am with sweats and palpitations. Now I understand why. Such a breakthrough for me as I have had broken nights for more than a decade.
    Thank you for your unusual approach to hypothyroid treatment. I take 50 mcg T3 daily and feel so much better following your advice.

  49. Latania October 4, 2019 at 2:24 pm - Reply

    I’ve recently started on t3-only thyroid hormone replacement. All my food “allergies” appear to have gone as a result! Amazing to be able to enjoy dairy again. It was hypothyroidism causing the reactions, not the food.

    • Amy November 30, 2019 at 7:02 am - Reply

      I just started on T3 only Cytomel. I quit taking my Levothyroxine and that seems to allow the T3 to work better( I was using both prior). Temps and pulse are up. I was wondering if you recommend continual/slow release or just dosed at multiple times of the day. I take it 3 times a day right now.

  50. Amy November 30, 2019 at 7:21 am - Reply

    On average, how long does it usually take to get to a point where dairy introduction goes well? 60 days or more. I’ve been diagnosed with a Hashimoto’s for almost 10 years. I’m incorporating your recommendations very slowly and just those small things I’ve done have had a definite positive impact, and that’s after just 2-3 weeks. I had problems with dairy since birth so I guess that indicates hypothyroidism at a very young age. I was just told I had a “weak constitution.” Never tested until my 30’s when I could not get out of bed due to severe fatigue. I don’t have lactose intolerance; my issues in my 30’s were with the whey component of milk. I have found I’ve done best with sheep’s milk/cheese products, but they still cause severe constipation and mucus production- just less than cow or goat milk. Despite all that I looove dairy and pray for the day I can tolerate it again. When I was vegetarian I ate tons of dairy…😞

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