The Autoimmune Protocol

The Autoimmune Protocol

Let’s talk food. Specifically, let’s talk Autoimmune Protocol food.


An Autoimmune Disease Diagnosis

I recently shared my Hashimoto’s Thyroiditis diagnosis, and what I’m doing about it. My first line of defense was supplements to combat my body’s inflammation. Next, while I determine my route for thyroid hormone supplementation, I’m working to heal my gut and immune system through an elimination diet called the Autoimmune Protocol.

The Autoimmune Protocol

The Autoimmune Protocol, or AIP, is a refined version of the Paleo diet that focuses on nutrient density and places stricter requirements on what foods you should and should not eat, at least temporarily. Medical biophysicist Sarah Ballantyne created this protocol and dedicates her career to understanding autoimmune disease and promoting healing through diet and lifestyle changes.

Under AIP, foods can be broken down into two groups: those that promote health and those that undermine it. Some foods are pretty self-explanatory: most vegetables, seafood, and grass-fed organ meats are health-promoting, while gluten-containing grains, peanuts, and soy products are health-undermining. Other foods are a little tougher to categorize, such as nightshades, eggs, nuts, and seeds.

The theory behind the Autoimmune Protocol is twofold: by removing all foods that may contribute to inflammation and gut irritation, you promote healing and immune system regulation through nourishing, nutrient-dense foods. Autoimmune diseases are typically linked to four main contributors: nutrient deficiencies and imbalances, poor gut health, hormone imbalances, and an immune system gone rogue. The Autoimmune Protocol removes all foods that may contribute to these triggers and gives your body a reprieve of sorts. Once your symptoms subside, whatever that looks like for you, you can reintroduce foods one at a time and see what, if any, trigger your symptoms.

What to Eat – and What Not to Eat

The Autoimmune Protocol uses the general Paleo diet as a template and builds upon it, excluding all foods that may activate the immune system or irritate the gut. These foods include:

  • Grains
  • Legumes
  • Dairy
  • Refined and processed sugars and oils
  • Eggs
  • Nuts
  • Seeds, including cocoa, coffee, and seed-based spices (Boohiss)
  • Nightshades: white potatoes (but not sweet potatoes!), tomatoes, eggplant, sweet and hot peppers, cayenne, red pepper, tomatillos, goji berries, and spices derived from peppers, such as paprika
  • Alcohol
  • NSAIDS (sorry, Advil)
  • Non-nutritive sweeteners (i.e. stevia)
  • Emulsifiers, thickeners, and other food additives, such as carrageenan in some almond milks and guar gum in some coconut milk products

So what can you eat?

  • All the vegetables! (minus the nightshades): it’s recommended to eat 8-14 cups of veggies per day
  • Fruit, but only 1-3 servings a day to limit fructose intake (unless you’re running an ultramarathon, then you eat all the dried blueberries)
  • Quality meats: grass-fed, pasture-raised, and wild meat as much as possible
  • Organ meat and offal (I’m still a little afraid of this one)
  • Herbs and spices
  • Good, yummy fats: avocado, grass-fed animal fats, fatty fish, olive, avocado, coconut, and palm oils
  • Probiotic/fermented foods
  • Glycine-rich foods: such as collagen peptides, bone broth, and that pesky organ meat
  • Natural sugars, such as maple syrup (thank goodness), honey, and blackstrap molasses (but in limited quantities)

Autoimmune Protocol and Eating Disorder Recovery

This is a little daunting, especially for someone who has a history of disordered behaviors around food. I learned about AIP months ago, when I was first diagnosed with Hashi’s, but I pushed it aside. It sounded too hard and too restrictive, and I was finally to a place where I could go out to eat without dragging guilt, shame, and fear with me. I’ve been gluten-free for seven years (years of GI distress led to a gluten-intolerance diagnosis long ago), but removing everything else (or so I thought) was too much. My eating disorder recovery process was too raw and vulnerable.

But the Autoimmune Protocol planted itself in the back of my mind. In the last month, AIP kept me awake at night, tossing and turning with indecision. I wanted to try it, to give it a fair shot and address some GI issues I’d been having (particularly around tomatoes, bell peppers, chickpeas, and lentils – see a trend?), but I was scared. Terrified. What if this triggered more restriction? What if this awakened a part of me – the disordered, restrictive, controlling part – that I try to keep at bay on a daily basis?

But, what if it didn’t? What if, like the 1,200 scientific studies denote, the Autoimmune Protocol does promote healing and alleviate my symptoms? What if I can address the root cause of my autoimmune disease and put it into remission? What if eating disorder recovery and autoimmune disease healing are not mutually exclusive?

So, I started the protocol. I hid all of my gluten-free flours and pastas, my lentils and grains, even the chocolate and hard ciders in the hardest-to-reach pantry in my kitchen. My many jars of nut butters and seeds are in a bag in the corner of my fridge. I brought all of my random candies and jars of peanut butter to community food table at work. I donated my tomatoes and peppers to friends. I started the Autoimmune Protocol.

Autoimmune Protocol: A Process 

It took three days to not accidentally eat something I wasn’t supposed to (sorry pea milk and Vega protein powder). On day 3, I threw a fit over a plate of uneaten kimchi (it had chili in it). On day 4, I almost cried over (a lack of) pancakes. On day 5 I realized it’d been four days since I had crippling fatigue or extreme mood swings. On day 6 I craved meat and avocado for breakfast and broke through a weeks-long plateau at the climbing gym. It wasn’t until day 7 that I thought I could maybe have a shot at doing this – and then on day 8 I nearly gave up, again.

It has been work. I rarely cooked meat before this (save for eggs), and making sure I have enough food to fuel my adventures and training is no easy feat, with or without the Autoimmune Protocol. While I am learning how to not overcook every animal product I touch, I’ve also had some major culinary successes, including a Valentine’s Day dinner of mint lamb burgers and sweet potato fries, and crowd-pleasing guacamole and plantain chips at my first AIP-era social outing.

I’m figuring out how to meal plan while allowing myself to continue honing my ability to decipher what my body craves and eat intuitively, an important skill to practice in my eating disorder recovery. I’m turning to podcasts and websites and books on healing and the Autoimmune Protocol, including my current favorite Mickey Trescott’s book The Autoimmune Paleo Cookbook and Trescott and Angie Alt’s book The Autoimmune Wellness Handbook.

Tracking the Elimination Phase

I’m committing to at least 30 days in the elimination phase of the Autoimmune Protocol and am keeping a journal of daily symptoms and notes on things such as training, energy levels, my menstrual cycle, and anxiety. I am also setting daily and weekly goals as I embark on my healing. AIP isn’t just about what you eat, it’s also about lifestyle, including adequate rest, addressing adrenal fatigue, and stress management.

In just a few days on the protocol, I am already discovering what foods leave me feeling good (avocado, squash, all sautéed greens) and those that leave me feeling not so great (more than one serving of broccoli, yams, and dates). I’m learning.

I’m also unpacking my emotional ties and relationship with food and eating – and how I can heal and mend this as well as my gut and immune system. Food has so much emotional weight and power – and I’ve found that in this process of resetting my diet, even temporarily, I am also resetting my relationship with food, mealtimes, and the act of eating. Under the Autoimmune Protocol, food is nourishment. It is not a source of guilt or shame, nor is it even a source of a tummy ache (usually). It is an opportunity to provide my body with what it needs, and only that. That is pretty powerful.

This week is my second full week on the Protocol, and my first with an actual plan. This is also the week I race a 50K, on an AIP compliant diet. We’ll see how this goes.

This week’s goals in healing and nourishing:

  1. Prepare more than enough food for my race Saturday, including dried blueberries, maple syrup, roasted sweet potatoes (not the orange kind!), and some post-race bone broth.
  2. Set a bedtime alarm of 9 pm and only hit snooze once (even if Lindsey Vonn is skiing).
  3. Pack real lunches for work each day. And accept that no, I cannot make this up on the fly like I used to.
  4. Find out of the box sources of grass-fed, pasture-raised meat within my budget.

Let’s raise our mugs of bone broth to healing.

When the immune system goes rogue: Hashimoto’s Thyroiditis

When the immune system goes rogue: Hashimoto’s Thyroiditis

Hashimoto’s Thyroiditis and Autoimmune Disease

I was covered in mud. Splatters of grime, red clay, and wet dirt speckled well past my running skirt. My shoes, once a deep purple, were a dark brown and squished over the singletrack. My breath was somewhere between labored and controlled, muffled by the steady rain and wind. Arms pumping, legs flying over the rolling terrain, I felt swift. Efficient. Determined. I was alone, running new trails and moving with a power I’d forgotten I have.

In the early miles of this run, I nervously avoided the puddles, toeing my way around the edges of the trail. Now, I barreled through, no longer avoiding the mess, no longer skimping on the opportunity to play.

Puddles, deep mud, and the occasional fallen tree were no match for my stride. My emotions and thoughts fueled every step, creating a cohesive thread of emotional response, mental calculation, and physical movement. This thread pulled me through phases of confusion and grief, anger and frustration, and finally, as I stomped through ankle deep mud, acceptance.

I was recently diagnosed with Hashimoto’s Thyroiditis, an autoimmune disease where the immune system attacks the thyroid. The diagnosis wasn’t necessarily a shock, however, the emotional weight of an autoimmune disease was. This diagnosis is the ankle deep mud. It is the puddle I tiptoed around, in fear of getting my shoes wet. It is unavoidable, unpredictable, and now splattered well past my knees. But I’m done avoiding the mud – I’m done pretending I don’t have an autoimmune disease. I want to heal, I want to play, I want to jump in some puddles.

So, let’s start talking about it. About autoimmune disease, Hashimoto’s, and my path toward healing.


Hashimoto’s Thyroiditis is an autoimmune disease where the immune system attacks the thyroid, leading to chronic inflammation and impairing the thyroid’s ability to do its (very important) job. Hashi’s is the leading cause of hypothyroidism in the US – a condition where the thyroid doesn’t make enough thyroid hormones to meet your body’s needs. Researchers aren’t entirely sure why some individuals develop autoimmune disorders such as Hashi’s and others do not. The likely cause is a combination of genetics, environmental triggers and toxins, and intestinal permeability (aka, “leaky gut”).[i] There are also studies linking this particular autoimmune disease with eating disorders.

Over 50 million Americans suffer from autoimmune disease, and of that 50 million, 75 percent are women. Once you develop one autoimmune disease, it becomes much, much easier to develop another. There are more than 80 types of autoimmune diseases, and many have very broad, all-encompassing symptoms, making diagnosis difficult.

In the case of Hashi’s, getting a definitive diagnosis can take years. In my case, it did.

What about this thyroid?

The thyroid is important. This little butterfly shaped organ nestled in the lower front of your neck controls the body’s most basic functions. Its main job is hormone production – thyroid hormones are multifaceted worker bees with too many accolades for a single page resume. They control the way your body uses energy and regulate breathing, heart rate, the central and peripheral nervous systems, body weight, metabolic rate, muscle strength, menstrual cycle, body temperature, and cholesterol levels, among other things. Every cell in your body is impacted by your thyroid hormones.[ii] When you have too much or too little of these hormones, your entire body is out of balance, and you can experience a slew of symptoms, including:

  • Fatigue and sluggishness
  • Trouble tolerating cold
  • Muscle aches, tenderness and stiffness
  • Joint pain and stiffness
  • Muscle weakness
  • Constipation
  • Pale, dry skin
  • Dry, thinning hair
  • Irregular menstrual cycles
  • Trouble getting (and staying) pregnant
  • Excessive or prolonged menstrual bleeding (menorrhagia)
  • Brittle nails
  • Hair loss
  • Acne
  • Trouble sleeping
  • Unexplained weight gain
  • Unexplained weight loss
  • Memory lapses and brain fog
  • Depression
  • Anxiety
  • Vertigo
  • Irritability, mood swings, and mood disorders
  • Nervousness
  • And, apathy, feeling emotionally numb

I am no stranger to these symptoms. I’ve been told to “keep an eye” on my thyroid hormone levels since high school – while also enduring an eating disorder, amenorrhea, and running many, many miles in an attempt to find solace in it all. After years of visiting physicians, nutritionists, gynecologists, acupuncturists, naturopaths, and my fair share of therapists, I finally have an answer (and I finally found a medical provider willing to dig a little deeper). I have Hashimoto’s Thyroiditis (with a side of sub-clinical hypothyroidism). I have an autoimmune disease. I thought I was healthy – and yet, I am not.

What comes with a diagnosis?

I am still settling into the diagnosis. Still working my way through nearly weekly diagnostic tests and doctor’s appointments. Still reading study after study on treatment options. Still learning. Still discovering. Still wondering, how did this happen? Why me?

While I could list the symptoms and share the years of daily struggles and anxieties I can now attribute to this disease, I want to talk about how I am feeling right now, and what I am doing about it.

I am relieved, scared, ashamed, and angry.

I am frustrated, tired, humbled, and overwhelmed.

When I first received this diagnosis, I pretended it didn’t exist. I shoved it under the rug with the fears and anxieties it prompted and assumed everything would be fine. My symptoms worsened, but every time I thought about the diagnosis, I felt sick to my stomach. I didn’t want to deal with it. I didn’t want to face my reality. So I didn’t.

And then things started piecing themselves together.

Symptoms worsened. Energy levels plummeted. I developed a sudden allergy and wound up in the hospital in anaphylactic shock. I shook with full-body chills throughout the winter. My situational anxiety and depression became not so situational. I developed severe cystic acne for the first time. The more I learn about the thyroid and Hashi’s, the more I realize just how much this disease controls my daily life.

Facing reality (and treatment)

Treatment began with a slew of supplements to combat the inflammation. I worked to incorporate more protein into my diet, ate more gut-healing foods, and got over my fear of kimchi. I researched treatment options, committed to routine blood work, and memorized the carpet’s pattern in my physician’s waiting room.

Despite these holistic attempts to combat inflammation, my thyroid hormone levels are still too low, and my thyroid antibodies (the sign of inflammation) are still too high. My symptoms remain, spontaneously shutting my entire system down with fatigue and unexplainable exhaustion. I’m now to the point of needing to supplement my body’s thyroid hormones – and am navigating my options on this front.

I’m committed to holistic medicine and addressing the root cause of this autoimmune disease, rather than solely placing a Band-Aid to mitigate my symptoms. That being said, at this point alleviating my symptoms is one of my top priorities. I am desperate for healing.

Phase One: Diagnosis

So, we’re at phase one: Diagnosis. And in this phase, I’ve struggled. I’ve grieved over the loss of the health I thought I had. Over my lost energy and fire. Over the years of tireless work and struggle to recover emotionally, mentally, and physically from an eating disorder, only to immediately have another struggle placed before me. I yelled, screamed, and kicked at the universe, demanding to know why. And then, I accepted my reality. I ran through the mud.

I am choosing to navigate my healing on my terms, to use this opportunity to learn more about my body and hear its subtle signs and signals. I’m excited to discover what nourishes me, and how I can provide my body the rest, fuel, and (potentially) hormone supplementation it needs.

My first stop? Food. Specifically, the autoimmune protocol. More on that to come.


[i] The Hashimoto’s Protocol, by Izabella Wentz 

[ii] The Hashimoto’s Protocol, by Izabella Wentz