This is for now.

I’m embarking on another elimination diet. I’m giving up all sugars (including raw honey), high glycemic fruits (I’ll miss frozen bananas!), all grains (no big change there), nuts and seeds (I’ll miss my daily almond or peanut butter on fruit..and macadamia nuts), all gluten containing compounds (already done), all dairy (for me this means raw milk, feta on Greek food, and Kerrygold butter), eggs (I usually have every morning), soy (already said goodbye to), fungi (I guess giving up mushrooms won’t be the hardest part), alcohol (in December? Bad timing…), beans and legumes (my neighborhood Mexican joint will have to wait), nightshades (you have no idea how common tomatoes are until you can’t eat them), coffee (Noooo! Not again! Teeccino here I come…), and all processed foods (the occasional bag of Trader Joe’s white cheddar popcorn would attack me- or vice versa). This time I’m following the RepairVite Program with the focus on healing leaky gut and discovering food allergies and intolerances. While I might not currently be feeling very inspired, I am, however, feeling very hopeful and looking forward to feeling great. I’ve been down the elimination diet road before and was hoping not to revisit so soon. But I’m willing to do everything that I think is best for my health and wellbeing, and I think it’s important to have experienced myself the things that I often suggest for clients. So here we go, onto round two!

A lot of people are unfamiliar with leaky gut and Hashimoto’s Thyroiditis, or don’t really understand how they’re connected. So here’s why this post might be of interest to you. Hashimoto’s is the most common form of thyroiditis, may be the most common form of hypothyroidism, and is one of the most common autoimmune diseases. Leaky gut (or “Hyperpermeable Intestines” if you prefer fancy terms) generally goes hand in hand with autoimmune conditions, since the gut-thyroid connection is so vital. Most of us could greatly improve our gut health, and we rarely realize poor gut health’s greater implications on our overall health.

Without getting into too many specifics, I’ll explain a little back story before my current situation. I’ve known that I’ve had hypothyroidism for about 7 years. I’ve always had nagging symptoms but my doctor would only look at the TSH lab (“Thyroid Stimulating Hormone”) instead of getting the whole picture. As my thyroid got worse (since the reason why it was suffering was not given any attention), she would just raise my dose of Levothyroxine (the common synthetic thyroid medication), and disregard my symptoms, complaints, and desire to understand why my thyroid was “tired”. For years I put up with this because I was told that the condition was common, that I was healthy, and because I didn’t know how to be my own health advocate.  I later learned that this approach is standard with most MD’s as well as harmful, as it completely allows the probable thyroid destruction going on behind the scenes to go untouched and make everything worse. My doctor never told me about Hashimoto’s Thyroiditis, let alone bother to check me for it (even though it was extremely likely that I had it at the time), because from a medical standpoint, the “treatment” (I use that word loosely here) would be the same regardless of whether I had it or not. While I don’t want to bash anyone in particular, I highly disagree with this method of “treatment” and am disappointed by the lack of care in this area. I learned about Hashimoto’s last year while I was studying to be an NTP- got myself tested and confirmed. No big surprise there. I learned about why this matters for my overall health and I began educating myself on the specifics of my condition as much as possible.

My first big deal discovery was the gluten-thyroid connection. The body confuses the protein found in gluten (gliadin) as your thyroid gland, so when gliadin enters the bloodstream, the immune system attacks both the gliadin and the thyroid gland. I heard Chris Kresser explain it once as a “case of mistaken identity” which made sense to me. This is always the case for when someone has gluten sensitivity (which, according to Dr. Fine is around 1 in 3 Americans), but it is becoming more well known how rare it is to find someone with Hashimoto’s that does not have some degree of gluten sensitivity. Considering those odds and knowing that standard lab tests for gluten intolerance are notoriously inaccurate (they only test one specific part of the gluten protein, when in reality person can be having an immune response to other parts of the gluten protein), it wasn’t worth it to me to get tested. I figured that even if I’m not gluten intolerant (very unlikely), I am better off without it. Whether or not you’re intolerant to it, it causes intestinal permeability (aka leaky gut) among other problems. I strictly gave up gluten cold turkey and a large amount of my health complaints- digestive and otherwise, faded away. Little annoyances that I never would have connected with gluten resolved themselves. A classmate of mine happened to be an expert of Hashimoto’s and between class and her blog and book wisdom, I quickly understood that giving up gluten and discovering any potential food allergies or intolerances (and removing them from my diet) was the first step in getting my Hashimoto’s under control.

In order to get to the root of any food allergies or intolerance that could be contributing to my condition, I decided to follow the Autoimmune Protocol. I decided to go on the diet for 2 months to treat it as an elimination diet, which is the best way to find out what your allergies and intolerances are. While I eliminated most of the same things that I am now during this time (although I think I kept eggs and nuts out of being overwhelmed), I didn’t follow the right protocol when adding foods back in. I basically was so excited to be done with the diet that I had a free for all and ate a couple of the things I was eliminating at the same time and didn’t give enough thought to how it made me feel. Well, that’s the most important part! So I never got an accurate reading of what specifically made me feel bad, although it was easy to say that I felt much better overall while on the diet than not.

So this time I’m doing it right! The RepairVite protocol is 2 weeks long, but that’s not quite enough time for an accurate elimination diet, so I’m extending the diet to 2 months. While I already suspected that I am consuming something I’m intolerant or allergic to, my recent blood test backed me up. My Eos (Eosinophil count) is high. Eosinophils are a type of white blood cell that are specifically involved in immune responses to infections caused by either parasites or allergic responses. A raised level indicates chronic inflammation resulting from the immune response. Chronic inflammation contributes greatly to leaky gut and Autoimmune issues. Yet another reason to rid my body of whatever I’m consuming that is causing this!

For the RepairVite protocol, what I am eating is just as important as what I’m not. Removing the allergens and stressors on the body is one very important part of healing leaky gut, but what I am eating does the actual healing part. Every morning I have a mug of the RepairVite supplemental powder, which is enzyme & amino acid based. It contains extremely gut healing nutrients that support the restoration and maintenance of the intestinal tract and gut lining. And as for healing foods? I’m consuming a ton of bone broth and meats that contain gelatin. I make my own sauerkraut and kombucha. I’m lucky to have 1/4 cow in our deep freezer (Crown S Ranch) and get weekly CSA vegetable shares from Jubilee Farm, so I can always cook up a quick meal if I don’t have time to plan ahead. I’m also incredibly thankful for avocados and sweet potatoes, since they’re allowed and I’m pretty sure I’ll never get sick of them.

The first couple of days weren’t too bad, although it was tough not to automatically snack on my usual things such as fruit and nuts. (And let’s be honest, I opened the can of peanut butter about 5 times a day and thought reeeally hard about just a tiny taste…and then I closed the jar super fast before I could.) Today is day 4 and I’ve never felt the effects of a detox so intensely. I’ve been getting more sleep than normal but am pretty consistently tired, and today my body and head have been aching all day. However, I do feel better than I have in a long time digestively. And an amazing change I’ve noticed is that already, my chronic runny nose that I’ve had for years is slipping away. Woah. I’ve put Crossfit on hold for a couple of months knowing that adrenaling my way through workouts would only make everything worse. I’m also not holding myself to any big running goals for now. It’s so hard for me to be gentle on my body and not constantly be pushing myself physically, but I know it’s the right thing for now. In fact, I’m pretty sure constantly trying to stretch my physical limits is what contributed to where I’m at now. I find the Balanced Bites ladies to be extremely knowledgeable and helpful and the last 10 minutes of Podcast #95 really hit home for me. They said “For some people, your body just hits this limit and what you used to be able to do you cannot do anymore. Or for some people the truth of the matter might be you just can’t do it right now. The same way I tell people who do, for example, an autoimmune protocol, if you’re not eating eggs and you’re trying to test and see and you’re so upset about it because you love eggs — or running — you know what?  Tell yourself this is for now.  This is while I heal and while I figure out what’s wrong with me.  Every person has to hit their rock bottom of deciding when you’re at that point where you’re ready to give up the thing that’s probably hurting you. And that’s that.”

So this is for now, and I’ll keep you updated on my results!

Below photos of my meals/snacks: sausage with purple cauliflower, bone broth, sardines and avocado salad with roasted veggies, roasted veggies hash with bacon and leftover turkey, roasted veggies with beef shank, cod fish with roasted veggies and salad, homemade kombucha, Whole Foods salad bar is great in a pinch, and sweet potato fries with avocado and salami.

photo (1)photo (2)photo (3)photo (4)photo (5)photounnamed (1)unnamed (2)unnamed


  1. Mickey

    So excited that you have decided to take the plunge into the autoimmune protocol, if for a second, more organized go! I am super impressed with your level of research and knowledge about everything. You have done an awesome job and I am sure others will be finding your experience valuable. Best of luck!!


  2. Angela

    Really interested to follow this with you, it’s something I should probably do but it feels really hard and overwhelming to remove some of my staples, already hard enough to find meals and snacks at times with the limitations I already place on my diet. And it’s the feeding kids CONSTANTLY that I find really hard! Good luck.

    • Emily

      Angela, I know what you mean about removing more foods when it can already feel difficult- adding feeding kids to the mix would definitely make things trickier. Have you checked out “The Paleo Mom” ( ) and her suggestions for paleo for kids? I think that most of the foods that I’m eating could be kid friendly, especially since they’re so simple. The book “Eat like a Dinosaur” is also a great resource. But what is most important to my success on the diet is planning ahead for each week to come. Good luck whenever the time is right for you!

  3. Joanna

    This is so great. I know I have to do this…I’m just talking to myself at the moment. I have leaky gut… I’ve had vitiligo for years, just been diagnosed with Hashimotos, but I’ve just had surgery to remove fibroids, so I’m being gentle with myself atm. I’ll get there…the new year for me I think.

    • Emily

      Joanna, the new year is right around the corner and a great time to start something big like this! Keep me posted how it goes for you!

  4. Louise

    I am struggling with similar issues – I do eat AIP – and I have added fodmap and gaps diet on top of this – I’m still gaining weight and not doing well. I take kombucha – I take probiotics – I switched over 6 months ago to natural desicated thyroid erfa – and this exasperated my adrenals – so I worked 6 months on adrenal health – and still trying to get optimal on NDT erfa. Not easy….what do you take for thyroid? What meds?

    • Emily

      Louise, glad to hear you’re giving AIP/low fodmap/GAPs a go but I’m sorry you still have symptoms. Are you working with an Endo/ND that you like? That was really helpful for me, as it becomes very tricky to try to piece this all together alone, no matter how educated you are. Blood tests are also important to find out what you could be missing that’s affecting you overall. I take Levo and Cytomel (both my T4 and T3 are low) as well as thyroid and adrenal supporting supplements. It’s also helpful in knowing if you’re TH1 or TH2 dominant before you start supporting your thyroid:

  5. Gayle

    Wow, Emily. This is a lot of great, useful information. Following your experience will be very helpful. Good luck.
    I like your food photos :-)

  6. joey

    Thank you for sharing that. You just told my exact story. AIP is tough but worth it.I’m still trying to figure out how to live without nuts too.

  7. hope

    I’m excited to follow your journey! this post took so very many words right out of my mouth. I was dx hashi’s in september, but, i have been on levo for 15 years! and i’ve been MISERABLE and NOT one doctor ever tried to put the 2 together, they just wanted me to take prozac or birth control and i refused. Anyway, i’m on day 71 of AIP and starting to feel better, but, i’m not there yet…. i’m excited to follow your journey! thank you for putting it all out there!

    • Emily

      Thank you for sharing Hope! I’m glad to hear you’re starting to feel better. I’m on day 14 so can’t imagine what 71 is like. Keep it up!

  8. Pingback: The Thyroid Sessions, Pt. 1 | Beets and Bacon

Post a comment

You may use the following HTML:
<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>