When we think about the Autoimmune Protocol, we often focus on what people feel: less fatigue, clearer thinking, fewer digestive issues, better mood, and improved quality of life. Those outcomes matter—but they also raise a deeper question:
What changes can we actually measure inside the body, especially in autoimmune thyroid disease—where labs may look “normal,” yet symptoms persist?
In Episode 65 of the Autoimmune Wellness Podcast, I continue the AIP Medical Research Review series with a breakdown of a 2023 clinical study from Poland that evaluated the Autoimmune Protocol for Hashimoto’s thyroiditis in a traditional academic setting.
What makes this study especially meaningful is that it expands beyond earlier research by assessing not only symptoms and thyroid labs, but also nutrient density, body composition, and thyroid ultrasound findings—offering a more complete picture of how AIP may support people with Hashimoto’s.
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Why This Polish Study Matters
In the first Hashimoto’s AIP study—the Abbott pilot trial—participants experienced significant improvements in symptoms and quality of life, even while thyroid hormone levels remained stable.
This Polish research team was inspired by those findings, but they wanted to explore additional questions, including:
- Does AIP support wellbeing without disrupting thyroid hormones in a larger group?
- Do measurable physical changes occur, such as changes in thyroid structure or body composition?
- Does nutrient intake shift significantly, and could that be one mechanism behind symptom improvement?
Instead of repeating the Abbott trial, this study expanded it—adding new layers that help us understand what might be happening under the surface.
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The Study at a Glance: What Was Examined
This was a 12-week dietitian-guided AIP Elimination Phase intervention in adults with Hashimoto’s thyroiditis.
Researchers measured outcomes before and after the intervention, including:
- Thyroid hormones (TSH, free T3, free T4, and others)
- Thyroid antibodies (TPO and thyroglobulin antibodies)
- Thyroid ultrasound imaging (thyroid lobe volume and structure)
- Body composition (weight, BMI, body fat, muscle percentage)
- Nutrient intake (macros, micronutrients, fiber, antioxidants)
- Symptom burden using a checklist of common Hashimoto’s symptoms
This combination of subjective and objective measures makes the Polish study a valuable companion to the Abbott trial.
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Who Participated—and Why It Matters
The study enrolled 28 adults with Hashimoto’s thyroiditis, almost all women (27 women, 1 man), with an average age in the mid-30s.
Importantly, participants were considered euthyroid, meaning their thyroid hormone levels fell within standard reference ranges—yet many still experienced significant symptoms. That “normal labs but still unwell” experience is extremely common in Hashimoto’s, and it’s exactly what both the Abbott study and this Polish trial set out to explore.
The researchers also excluded participants who had used elimination diets recently, helping ensure AIP was a truly new intervention for this group.
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The AIP Intervention: What They Actually Did
Participants followed a 12-week AIP Elimination Phase, guided by a research dietitian.
The intervention aligned closely with Core AIP elimination principles, removing commonly excluded groups such as:
- eggs, dairy, grains, legumes, nightshades
- highly processed foods and additives
Participants were given:
- a written allowed/avoided foods list
- example menus
- individualized meal plans tailored to energy needs
Unlike the Abbott trial—which used a staged transition and included broader lifestyle coaching—this study focused primarily on the dietary intervention and ran elimination for a full three months.
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Results: Nutrient Density Increased Dramatically
One of the most striking contributions of this study is that it quantified nutrient density—something we often talk about with AIP, but rarely see measured so clearly.
Calories stayed roughly the same, but nutrient intake changed substantially:
- protein increased as a percentage of calories
- fiber increased
- many vitamins, minerals, and antioxidants increased dramatically
The biggest takeaway here: participants didn’t improve because they ate less—they improved while eating similarly in calories, but with a much more nutrient-dense dietary pattern.
This matters because symptoms like fatigue, mood issues, hair and skin changes, and digestive complaints can be strongly influenced by micronutrient status.
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Results: Thyroid Labs, Antibodies, and Ultrasound Findings
Because participants were euthyroid at baseline, the study offered insight into how AIP may impact thyroid markers without pushing people into hypothyroidism.
Key outcomes included:
- TSH decreased (remaining within reference ranges)
- free T3 and free T4 decreased modestly (also remaining within reference ranges)
- antibodies shifted in mixed directions, without statistically significant change
A unique feature of this trial was thyroid ultrasound, which showed a small but measurable reduction in thyroid lobe volume over the 12 weeks—suggesting the possibility of reduced inflammation in the gland itself.
While ultrasound findings don’t “prove” mechanism, they add an objective data point beyond symptom reports.
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Results: Body Weight and Body Composition Improved
Despite the study not being designed as a weight-loss intervention, participants experienced meaningful improvements in body composition, including reductions in:
- body weight
- BMI
- body fat percentage
This occurred alongside stable thyroid hormone levels—suggesting metabolic improvements can happen without calorie restriction and without negatively impacting thyroid function.
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Results: Symptoms Improved Across the Board
Participants reported major decreases in many common Hashimoto’s symptoms—especially those that often persist despite “normal” labs.
Some of the most notable improvements were in:
- tiredness and fatigue
- brain fog / impaired concentration
- digestive symptoms (gas, bloating)
- dry skin and hair loss
- joint pain and muscle cramps
- perceived weight gain
Even though symptom tracking wasn’t done using a validated questionnaire, the overall pattern was clear: most participants felt noticeably better after 12 weeks on AIP.
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How This Compares to the Abbott Trial
Together, the Abbott pilot study and this Polish clinical trial tell a consistent story:
- Symptoms and quality of life can improve significantly even when thyroid hormones stay within reference ranges.
- AIP appears safe and feasible across different clinical settings.
- Nutrient density is likely a major driver of improvement—not just elimination.
- Antibodies fluctuate and don’t reliably correlate with symptoms, especially in the short term.
- This Polish study adds new evidence through ultrasound and body composition outcomes.
This is exactly what many people with Hashimoto’s experience: meaningful improvements in daily functioning that may not show up immediately—or clearly—in standard thyroid labs.
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Practical Takeaways for Hashimoto’s
If you’re considering AIP for Hashimoto’s today, this study reinforces several important points:
- Give yourself enough time (a 1–3 month elimination window can be a meaningful starting point)
- Track progress through symptoms and quality of life, not just labs
- Don’t use antibodies alone as your “scorecard”
- Focus on nutrient density—what you add matters as much as what you remove
- Metabolic improvements can occur without calorie restriction
- Objective inflammation-related changes may happen even when labs don’t shift dramatically
AIP isn’t a cure—but these studies add meaningful evidence that it can be a powerful supportive framework for people with Hashimoto’s.
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AIP Foundation Series: Learn the Framework
If you’d like help applying AIP safely and effectively, the AIP Foundation Series is a great place to start.
This free, 5-day email course includes:
- printable food lists
- beginner-friendly meal plans
- clear guidance on Core vs. Modified AIP
- tools to reduce overwhelm
👉 Sign up for the AIP Foundation Series:
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The New Autoimmune Protocol (Coming Soon)
If you want a deeper dive into the science and structure of today’s AIP, my upcoming book, The New Autoimmune Protocol, brings together:
- updated medical research
- clear guidance on Core vs. Modified AIP
- step-by-step planning tools
- updated recipes and meal plans
👉 Pre-order The New Autoimmune Protocol!
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Listen to the Episode
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Episode Timeline
00:00 – How AIP reached Poland
02:16 – Overview of the Polish Hashimoto’s study
03:54 – Hashimoto’s refresher: euthyroid but symptomatic
05:05 – Why the researchers wanted to study AIP
06:23 – Study participant profile
07:23 – The AIP intervention design
10:15 – Clinical measures and nutritional assessment
13:11 – Results: nutrient density
15:54 – Results: thyroid hormones, antibodies & ultrasound
18:15 – Results: body weight and body composition
20:11 – Results: symptom improvement
22:13 – Nutrient–thyroid marker relationships
23:23 – Interpreting thyroid hormone and antibody changes
25:53 – How this study compares to the Abbott trial
29:54 – Practical takeaways
33:06 – Recap and wrap-up
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Episode Transcript
Below is the full transcript of Episode 65 of the Autoimmune Wellness Podcast.
This transcript is provided for accessibility and reference.
AIP for Hashimoto’s: The Polish Study on Nutrient-Density, Symptoms & Thyroid Health (Ep 065)
[00:00:00] Introduction: When AIP Reached Poland
In our last Hashimoto’s research episode, we talked about a study that was very close to home for me, the Abbott trial, a community-funded project that Angie and I helped bring to life alongside Dr. Rob Abbott. That study showed that a structured AIP diet and lifestyle intervention could significantly improve symptoms, quality of life and inflammation in women with Hashimoto’s who are technically euthyroid on paper.
Today’s study is just as exciting for a different reason. A research team in Poland read about the Abbott trial, looked at the publicly-available information on AIP, and decided to design their own clinical study to test it: independently, in their own academic setting, and with their own patients.
They took the concept of AIP, translated it into their clinical context, and honestly, they did a really incredible job. And not only that, but the study was about twice as large in terms of participants and it added several layers that we didn’t see in the Abbott paper. In addition to the symptoms and thyroid markers, the Polish team looked at nutrient density, so how people’s vitamin, mineral and macronutrient intake changed on AIP. Their body composition, so they looked at shifts in body weight and body fat. And then also thyroid ultrasound, which gave them a glimpse into changes in the thyroid gland itself.
And of course, they still looked at those thyroid hormones and antibodies, plus the symptom changes and overall wellbeing. So in a lot of ways this study acts like a companion to the Abbott trial. Same general idea, meaning AIP for Hashimoto’s in euthyroid patients, but with a different research team in a different country, and using a slightly different design and a richer set of measurements. It’s a glimpse into what happens when AIP starts to be tested by outside researchers who simply find it interesting and potentially helpful.
Welcome back to the Autoimmune Wellness Podcast. I’m your host, Mickey Trescott, and this is another episode in our AIP Medical Research Review series where I walk you through the published clinical studies on the Autoimmune Protocol: what they examined, what they found, and what it all means for people living with autoimmune disease right now.
[00:02:16] Episode Overview: The Polish AIP Study
Today we’re diving into a Polish study that evaluated AIP for Hashimoto’s thyroiditis in an academic setting. We’re going to look at who participated, how the AIP intervention was structured, what changed in terms of symptoms, thyroid hormones, antibodies, thyroid ultrasound findings, body composition and nutrient intake, and how these results compare to what we saw in the Abbott trial.
As always, this podcast is for educational and informational purposes only and is not intended as medical advice. Be sure to talk to your healthcare provider before making any changes to your treatment plan.
In today’s episode, we’re exploring the second clinical study published on the Autoimmune Protocol for Hashimoto’s thyroiditis.
The name of the paper is Effects of an Autoimmune Protocol AIP Diet on Changes in Thyroid Parameters in Hashimoto’s Disease, published in 2023.
If you’d like to read along, I’ve included a direct link to the open-access study in the show notes.
We’re going to walk through the full study design: who participated, how the AIP intervention was implemented in this academic setting, and the broad range of outcomes that the researchers measured. Then we’ll break down the results, including shifts in symptoms, thyroid hormone levels, antibody patterns, nutrient density, body composition, and even those thyroid ultrasound findings.
By the end of the episode, you’ll have a clear understanding of what this research team discovered, how the results compare to the Abbott trial, and why the study represents an exciting next step in the growing global interest in AIP for autoimmune thyroid disease.
[00:03:54] Understanding Hashimoto’s – A Quick Refresher
Before we jump into the study, here’s a very quick refresher on Hashimoto’s and why this research is important. Hashimoto’s is an autoimmune condition where the immune system attacks the thyroid gland, thyroid hormone levels, things like TSH, free T4, free T3 can remain normal for years, even while the autoimmune process is still active, diagnosis often includes thyroid antibodies like TPO and Tg, which confirm that the immune system is involved.
The challenge is that many people with Hashimoto’s continue to feel unwell, even when their labs look fine. So they will have symptoms like fatigue, brain fog, digestive issues, mood changes, and weight fluctuations, and very commonly these are not explained by hormone levels alone. And this is the group that both the Abbott study and these Polish researchers focused on. People who were medically stable on paper, but still dealing with significant symptoms.
So with that quick refresher, let’s talk about why the Polish team wanted to study AIP, and how their approach adds something new to what we already know.
[00:05:05] The Questions the Polish Team Wanted to Answer
After the Abbott study was published, it sparked interest well beyond the AIP community, including this dietitian led research team in Poland. They saw the promising improvements in symptoms and quality of life and wanted to explore AIP further, but with a slightly different focus.
Here’s what they wanted to know. First, what AIP support wellbeing without disrupting those thyroid hormones? The Abbott trial showed stable thyroid labs, but the group was pretty small. The Polish team wanted to test this in a larger cohort of also euthyroid patients.
Second, the researchers wanted to understand whether AIP was associated with physical changes in the body itself, particularly in the thyroid gland and overall body composition. To explore this, they added thyroid ultrasound imaging to assess changes in thyroid volume, along with the standard anthropometric measurements to see how physiology shifted over time.
And lastly, how does AIP change nutrient intake? They suspected that increases in nutrient density might be one mechanism of improvement. So they performed detailed dietary analysis. In other words, the Polish team wasn’t repeating the Abbott trial. They were expanding it, asking new questions about thyroid structure, nutrient density, and how AIP performs in a more traditional medical setting.
[00:06:23] Study Participant Profile
With that background, let’s take a look at who actually participated in this Polish Hashimoto study. This trial enrolled 28 adults with Hashimoto’s thyroiditis. As is very common with this condition, the vast majority were women, 27 women, and one man with an average age of 35 years, ranging from 23 to 55.
And importantly, the researchers excluded anyone who had used an elimination diet in the past year. This means that participants were approaching AIP as a new intervention, similar to the design of the Abbott study. People were also excluded if they were pregnant or breastfeeding, had celiac disease, severe chronic illness such as renal or liver failure, malnutrition, eating disorders, or had implanted medical devices like electro stimulators.
So taken together, this group represents a very common clinical picture in Hashimoto’s: working-age adults, mostly women, medically stable, not new to the disease, and still seeking ways to feel better.
[00:07:23] The AIP Study Intervention
Next, let’s look at how the Polish research team structured their AIP intervention, because this tells us a lot about how participants actually implemented the protocol and how closely it aligns with the version of AIP used in other studies.
This was a 12 week dietary intervention guided by a dietitian, and based on the core principles of the Autoimmune Protocol Elimination Phase, as originally outlined by Dr. Sarah Ballantyne. The focus here was on nutrient density, whole foods, and avoiding ingredients that may contribute to immune dysregulation, gut irritation, or disruption of the gut microbiota.
The Polish team removed the same food groups that we exclude in Core AIP: eggs, dairy, cereals, grains, nightshades, legumes, food additives and highly processed foods, food containing lectins, which is their terminology, I think that originates, way back in AIP’s history. We don’t really use that anymore, but this captures the broad AIP elimination pattern in a slightly simplified academic format.
Participants were also encouraged to eat foods that support the microbiome, the intestinal mucosa and overall nutrient density. Their individualized AIP plans emphasized a variety of whole, unprocessed foods, fermented foods, and foods described as live, such as pickled or naturally cultured, foods free from heavy processing or high heat industrial preparation, gluten-free flours when needed, such as coconut and arrowroot.
And while this paper doesn’t detail every addition the way that the Abbott study did, the overall emphasis aligns with AIP fundamentals: whole foods, nutrient density, gut support, and avoidance of these extra things that we know can be problematic for people with autoimmune disease.
So next let’s talk about how the diet was delivered. Unlike the Abbott trial, which included coaching, group support and a staged six week transition, the Polish study used a 12 week Elimination Phase guided by a dietitian. So there was no phased transition described. Participants followed their individualized AIP menu from the start. So this is a much longer timeframe in elimination, this is three months, versus one month.
And the paper notes that each participant received a written list of excluded and allowed foods, an example menu, and then in an individualized AIP plan that was developed by the research dietitian. So this intervention was a little less lifestyle focused and more strictly nutritional and only focused on the Elimination Phase, but for far longer than the prior studies. So again, that 12 weeks versus the five and four from the IBD and Hashimoto’s trials.
[00:10:15] Clinical Measures & Nutritional Assessments
Now to understand what changed during the 12 week AIP intervention, the Polish research team used a comprehensive set of assessments including thyroid labs, the ultrasound, body composition markers, nutrient intake, and symptom tracking. These measures help us understand both how people felt and what was happening physiologically.
First, they completed thyroid hormone and antibody testing, so before and after they completed a full thyroid panel including: TSH, total T3 and T4, free T3 and T4 anti-thyroglobulin and anti-thyroid peroxidase antibodies. These markers allowed the researchers to monitor thyroid function and autoimmune activity throughout the study.
Next, a unique aspect of this trial was the inclusion of thyroid ultrasound imaging. Clinicians measured the size of both thyroid lobes and the structural appearance of the thyroid gland. Ultrasound is commonly used in Hashimoto’s to evaluate the degree of inflammation and long-term tissue changes. So this added an important structural dimension to the research.
Participants also underwent body measurements before and after the intervention. They took their weight, their BMI, their body fat and muscle mass via bioelectrical impedance, their height, and these assessments in the clinic allowed the researchers to evaluate changes in weight, fat mass, and overall metabolic health.
Another distinctive feature of this study was the detailed analysis of nutrient intake. Before beginning AIP participants completed a three day food record to document their usual diet. The research team calculated their calorie intake, their macronutrients, their fiber, and their micronutrient intake. And then using these data the dietitian created individualized AIP menus tailored to each participant’s energy needs, calculated using the Harris-Benedict equation and their physical activity levels. And then they also used the Polish Nutrient Intake Standards.
Participants continued any supplements or medications. The AIP menu itself was nutritionally balanced, so the the researchers did not recommend any supplements to be added.
For symptom tracking participants also rated their subjective wellbeing by reporting on symptoms commonly associated with Hashimoto’s, such as: fatigue, digestive symptoms, mood issues, cognitive changes, skin and hair changes, muscle and joint pain. These reports were collected before and after the intervention to assess how people felt alongside all of those lab work and the ultrasound results.
And then adherence to the intervention was supported through remote contact with the dietitian, monthly online check-ins, ongoing menu review and adjustment, and this allowed the researchers to monitor compliance without requiring in-person visits.
[00:13:11] Results – Nutritional Intake
Okay, so now the fun part, onto the results. We’ll begin by discussing nutrient density. One of the most exciting parts of this Polish study is how clearly it showed the nutritional shift that happens when somebody moves from a standard diet to the Autoimmune Protocol. And this is something that we often talk about in theory, but here we get to see it measured as this was a new feature of this study.
So even though the total calories stayed almost identical from before and after AIP, the average went from 2,067 calories to 1,997 calories per day, the balance of macronutrients changed in meaningful ways. Protein increased from 16% to 24% of calories, fat decreased from 33% to 30%, and carbohydrates stayed almost the same, shifting only from 45% to 44%.
So this combination– higher protein, modestly lower in fat, and stable in carbohydrates –reflects what we see when people increase whole foods like vegetables, roots, fruits, seafood, and high quality meats and reduce processed foods.
But the most striking changes weren’t in the macronutrients. They were in the micronutrients, and this is where AIP really shines. The study found major increases in nearly every vitamin, mineral and antioxidant measured.
Compared to the participant’s baseline diets, AIP led to: a five times increase in betacarotene, which is a precursor to vitamin A, a 50% increase in dietary fiber, a three times increase in vitamin A and a nine times increase in vitamin C. And then also they found significant increases in a very long list of essential nutrients, including things like folate, potassium, magnesium, iron, B vitamins, omega-3 fatty acids and antioxidant rich plant compounds.
So if you are reading along with a study, definitely take a look at table 2A for all of those nutrient categories and exact values.
So this confirms something we’ve known for years. AIP is incredibly nutrient dense. And a reminder, these participants were not eating less, they were not eating more. They were eating the same number of calories. They weren’t relying on supplements. They were just eating a true, whole food, anti-inflammatory diet, and their nutrient intake skyrocketed.
This matters because many symptoms in Hashimoto’s: fatigue, mood issues, hair and skin changes, digestive complaints can be heavily influenced by micronutrient status.
[00:15:54] Results – Thyroid Hormones, Antibodies & Thyroid Volume
Now let’s look at what happened to thyroid hormones, thyroid antibodies, and thyroid gland volume over that 12 week intervention. These are core markers for Hashimoto’s, and they help us understand how the body responds physiologically to the AIP dietary pattern.
So all of these participants began the study euthyroid with thyroid hormone levels already in the normal range. After 12 weeks of AIP, the TSH decreased by 27% from 3.72 to 2.69. Free t3 decreased by 13%, free t4 decreased by 11%.
Now, I will note here that even though these participants were classified as euthyroid, the standard reference ranges for TSH are controversial, especially in the functional medicine community. So most providers now consider a TSH of three to be problematic, and many narrow that window down to 2.5. So by functional medicine standards, I actually think that these patients could have been categorized as subclinical or mildly hypothyroid, and seeing them come back down closer to that 2.5 cutoff is actually a really great result.
And then importantly, even though those free thyroid levels decreased marginally. All of these values remained within that standard reference range, which means that the thyroid function stayed mostly stable overall. These small decreases occurred without pushing anyone towards hypothyroidism.
Now, the antibody results were mixed, and they did see an increase in anti TPO and a decrease in anti-thyroglobulin, and both of these changes were not statistically significant, but they are very interesting and we will discuss them a little bit later.
And then one of the most interesting additions in this Polish study was thyroid ultrasound, which allowed researchers to measure changes in the size of the thyroid itself. So after 12 weeks of AIP, the right thyroid lobe volume decreased by 5.3%, and the left thyroid lobe volume decreased by 6.2%. A reduction in the thyroid volume can reflect decreased inflammation or reduced immune activity within the gland.
[00:18:15] Results – Anthropometric Changes
Another key area the Polish research team examined was how body weight and body composition changed over the 12 week AIP intervention. These measurements offer insight into metabolic shifts, inflammation, and overall health trends during the study. The results were statistically significant across every measure.
So first, body weight and BMI decreased. After 12 weeks on AIP body weight decreased by 4.83%, so that’s about roughly eight pounds on average. BMI decreased by 5%, which brought a lot of these participants closer to the normal range for BMI, even though this intervention was not designed as a weight loss program.
Body fat percentage decreased by almost 10%. Nearly a 10% reduction in body fat over 12 weeks is substantial, especially without intentional calorie restriction. This suggests improvements in metabolic efficiency, inflammation, and overall diet quality.
Now, body muscle percentage did decrease by 4% and this decrease appears to be relative to overall fat loss and total weight reduction, rather than a true drop in lean mass.
So how do we piece all of this together? I think that even though the AIP diet was not designed as a weight loss intervention, participants experienced meaningful improvements in their body weight, their body mass index, their body fat percentage, and these are things that are all a primary concern for patients with Hashimotos.
All of the changes were statistically significant and reflect the shift towards a more nutrient dense, less inflammatory, whole food dietary pattern. And importantly, these findings occurring alongside stable thyroid hormone levels suggest that there’s something about the diet that is supporting metabolic improvements without negatively impacting thyroid function.
[00:20:11] Results – Symptom Burden
The Polish research team also examined changes in daily symptoms, not with a validated tool like the Short Form 36 or the MSQ, but through a simple checklist of common Hashimoto’s-related symptoms. Participants indicated whether they were experiencing each symptom before beginning AIP, and then again after the 12 weeks.
While this approach isn’t standardized, it does give us a helpful snapshot of how people felt during the intervention. At baseline, many participants were dealing with a wide range of classic Hashimoto symptoms. The most frequent were: 82% experiencing tiredness, 71% experiencing dry skin, 71% experiencing brain fog, 64% experiencing drowsiness, 64% experiencing hair loss, and 61% experiencing intestinal gas and flatulence.
So these numbers reflect what we commonly hear from people with Hashimoto’s who are technically euthyroid, but still have all of these symptoms, right? And after the intervention, the percentage of participants reporting many of these symptoms decreased dramatically.
Some of the biggest changes included that tiredness going from 82 to 29%, impaired concentration from 71 to 18%, which I think is just amazing. Flatulence from 61 to 29%, gas, 61 to 21%, fatigue from 50 to 11%, dry skin from 71 to 32%, hair loss from 64 to 32%, joint pain from 57 to 21%, weight gain from 57 to 11%, and then muscle cramps from 43 to 7%.
And this trend is unmistakable, the majority of participants felt noticeably better after 12 weeks on AIP. They experienced improvements in energy, cognition, digestion, skin and hair, joint pain, and overall sense of wellbeing, all while maintaining those stable thyroid hormone levels.
[00:22:13] A Note on Nutrient–Thyroid Marker Relationships
So next on note on thyroid-nutrient marker relationships. The Polish research team also explored whether changes in specific nutrient intake were linked to changes in thyroid hormones, antibodies, or thyroid ultrasound findings. This analysis was very exploratory, but it produced some interesting points.
For example, they found that increases in manganese intake were associated with decreases in TSH. Vitamin D, iodine, vitamin C, folate, and even caffeine intake were all linked to changes in free T3. Long chain omega-3 and omega-6 fatty acids were the strongest predictors of changes in free T4. And surprisingly retinol, which is vitamin A and the amino acid isoleucine, were tied to shifts in anti TPO antibodies.
Now it’s important to note that these models don’t prove cause and effect, but they highlight just how nutritionally sensitive thyroid physiology may be. And if you’re curious about the full list of nutrient relationships or you want to see the detailed equations, you can find all of it in the tables and supplementary materials of the published paper linked in the show notes.
[00:23:23] Interpreting the Thyroid Hormone & Antibody Results
Now that we’ve reviewed all of the data, let’s take a moment to unpack what the thyroid hormone and antibody changes might mean. Because this is an area where Hashimoto’s patients and clinicians often have a lot of questions. In this study, TSH, free T3, and free T4 all decreased modestly over the 12 week AIP intervention.
Importantly, all of the hormone levels remained fully within the conventional reference ranges with a side note that by functional medicine standards, the mean of this group was actually outside what is considered a good TSH before the study, but that came back into the normal range by the end of the intervention. And that’s just my analysis.
This mirrors what we saw in the Abbott study: AIP didn’t disrupt thyroid function and hormone levels stayed stable and healthy. When hormones move slightly within the normal range without crossing any of those thresholds, it generally reflects natural day-to-day physiological variation, especially when body weight decreases as it did here. Weight loss alone is known to shift thyroid hormones modestly downward, even in people without thyroid disease.
So those antibody results were a little more complex. Again, neither of these changes reached statistical significance, but the increase in TPO naturally raises eyebrows, and I think it’s important to interpret in this context. Antibodies can fluctuate a lot naturally and sometimes very dramatically. Short term studies commonly show swings in both directions, even without any intervention. And it is my feeling that antibodies do not reliably correlate with symptoms.
This is still a very open question in Hashimoto’s research. It is clear that Hashimoto’s patients can feel terrible sometimes with low antibodies, and sometimes we can feel really great with high ones. In both the Abbott and this Polish study, participants experienced major improvements in their symptom burden, regardless of their antibody levels, which I think is a very key point to hone in on.
So when we put these findings together with the Abbott study, one message becomes clear: quality of life, symptom improvement, and overall metabolic health are often much more meaningful indicators of progress than those short term changes in antibody levels. This aligns very much with what clinicians and AIP Certified Coaches regularly see in practice and what many patients report experiencing themselves.
[00:25:53] How These Results Fit With the Abbott Study
Now that we’ve reviewed the findings, let’s look at how this Polish study fits alongside the Abbott Pilot trial, the first ever AIP study for Hashimoto’s, and what we can learn by comparing the two. Across both studies, a consistent pattern emerges.
First symptom improvement happens even when thyroid hormone levels are normal. Both studies enrolled participants who were euthyroid at baseline, meaning their thyroid hormones were already within those standard reference ranges, and yet, in both studies, participants reported significant improvements in symptoms and overall wellbeing.
This mirrors what many practitioners in the AIP Certified Coach community report in real world practice. Clients with Hashimoto’s often feel dramatically better when nutrient density increases and inflammatory triggers are removed. Even when their labs haven’t budged. This reinforces a key message for Hashimoto’s care: symptoms and lived experience can improve significantly independent of those thyroid hormone levels.
Number two, AIP appears safe and well tolerated across different settings. Neither study reported serious adverse effects and both demonstrated strong adherence. However, adherence was higher in the Abbott study, likely due to the multidisciplinary support model, which included that weekly coaching, group community support, structured education, and close practitioner contact. By contrast, the Polish study used a more traditional dietitian guided model with remote check-ins and still achieved meaningful improvements. This suggests that AIP can be successful and both high support and standard clinical environments, although more support may lead to greater consistency.
Three, both studies point to nutrient density as a key driver of improvement. The Abbott study emphasized nutrient dense eating, but did not measure micronutrient intake. The Polish study did, and the increases were absolutely striking. Together these studies strengthen the hypothesis that nutrient density, not just eliminations, plays a central role in symptom improvement for people with Hashimoto’s.
Number four, antibody findings differed and should be interpreted with caution. The Abbott study showed a small, non-significant downward trend in antibodies. The Polish study showed a non-significant increase in one and a decrease in the other.
It’s important to be measured here. Antibodies can naturally fluctuate. They don’t consistently correlate with symptom burden. And so those short-term changes up or down are not reliable indicators of long-term autoimmune activity. So I think that these two studies together reinforce that antibody levels shouldn’t be the primary measure of whether someone with Hashimoto’s is improving using AIP.
Number five, the Polish study contributes something new: objective, structural and metabolic changes. This study uniquely included the thyroid ultrasound showing a 5 to 6% reduction in thyroid gland volume over 12 weeks, and unlike symptom reports, ultrasound is a non subjective indicator, suggesting that something physical shifted inside the thyroid gland itself, potentially reflecting that reduced inflammation.
In addition, participants lost about eight pounds on average, they reduced their body fat by nearly 10%, despite eating roughly the same number of calories that they were before. And at the same time, those thyroid hormones remained stable and within the normal range. So these changes– stable hormones, reduce thyroid gland volume, improvements in weight and body composition– point to a broader metabolic and inflammatory benefit that aligns with what many people report subjectively.
Together these two studies paint a cohesive picture that AIP might offer a meaningful support for people with Hashimoto’s who feel unwell despite those normal looking labs. And this has now been demonstrated in two independent clinical settings.
[00:29:54] Practical Takeaways for Listeners
What does all of this mean if you are considering using AIP to support your Hashimoto’s symptoms today? Across the Abbott study and this newer Polish study, several themes emerge.
Number one, make sure to give yourself enough time. Four to 12 weeks is a meaningful window. In the Abbott study, participants saw improvements within four to 10 weeks. In the Polish study, the intervention lasted 12 weeks with significant benefits. Together, these support the current guidance that a one to three month Elimination Phase is a solid starting point for many people with Hashimoto’s.
Number two, your best indicators of progress are going to be symptoms and quality of life. Both studies showed improvements in fatigue, brain fog, digestion, skin and hair symptoms, mood and overall daily functioning. And importantly, these improvements happened even when thyroid labs did not shift. So pay attention to how you feel, your energy, clarity, sleep, digestion, and mood. Those day-to-day changes tell you far more than a lab value does in those early weeks.
Number three, don’t worry about those antibody levels after diagnosis. Antibodies fluctuate naturally, don’t correlate reliably with symptoms, don’t predict how you’ll feel, and don’t change much in the short term. So if you’re feeling better, sleeping better, thinking more clearly, and living with fewer symptoms, that is real progress even if your antibody levels stay the same or temporarily tick up a bit.
Number four, nutrient density is not optional, it is essential. Both studies emphasized nutrient-dense eating and the Polish study quantified it. This reinforces a core AIP principle: what you add is just as important as what you remove. Loading your diet with vegetables, fruits, quality proteins, seafood, organ meats, roots, herbs, spices, and fermented foods is one of the most powerful parts of AIP and likely a big reason that some people feel so much better.
Number five, safe weight loss and body composition changes can happen naturally without restricting calories or doing a weight loss diet. Participants in the Polish study ate roughly the same amount of calories, lost an average of eight pounds, and reduced body fat by nearly 10%. This supports what we teach in AIP: you don’t need to do AIP for weight loss, you don’t need to restrict calories during elimination. When nutrient density goes up and inflammation goes down, the body often finds a healthier metabolic balance on its own.
Number six, inflammation can improve even when thyroid labs do not. Both studies included objective measures that captured inflammatory change. Hs-CRP decreased in the Abbott study and thyroid gland volume decreased on ultrasound in the Polish study. These are physical, measurable indicators that something real is shifting in the body, even when that TSH, T4 and T3 remain the same. This is reassuring for anyone who feels better on AIP but doesn’t see proof in their thyroid labs.
AIP provides a structured, nutrient dense, anti-inflammatory framework that has now been shown in two independent clinical studies to meaningfully support people with Hashimoto’s.
[00:33:06] Recap and Wrap-Up
So let’s quickly recap what we covered today. We talked about who was studied: 28 adults with Hashimoto’s, all medically euthyroid, yet still experiencing symptoms that so many Hashimoto’s patients know well– fatigue, brain fog, digestive issues, skin changes, and more.
We reviewed what changed: after 12 weeks on AIP, participants saw clear improvements in their daily symptoms and overall wellbeing. They experienced healthy weight loss and nearly 10% reduction in body fat even without lowering their caloric intake. Thyroid hormones stayed stable, and ultrasound showed a 5 to 6% reduction in thyroid gland volume, suggesting a physical reduction in inflammation.
And we explored why it matters: these results align closely with the Abbott study, showing that AIP is safe, feasible, and genuinely helpful for people with Hashimoto’s. Improvements in symptoms, mood, digestion, and energy can happen regardless of changes in thyroid labs or antibodies and nutrient density appears to play a major role.
Thank you so much for listening, if you enjoyed this episode, please subscribe so you don’t miss the rest of the Medical Research Review Series. Ratings and reviews on your favorite platform truly help this information reach more people.
And don’t forget to download my AIP Foundation Series at theautoimmuneprotocol.com/foundations. It’s a free five day email course with over 60 pages of resources and automatic updates whenever a new AIP study is published.
And if you are feeling inspired by the research we explored today, I think you will really appreciate my upcoming book. It’s called The New Autoimmune Protocol, and it is arriving in May. It distills all of the latest science into a clear, practical guide, complete with new recipes and meal plans to support you from day one. You can pre-order your copy now and your support truly helps this work find the people that it’s meant for.
Thank you again for joining me, and I will see you next time!
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References
Abbott, R. D., Sadowski, A., & Alt, A. G. (2019). Efficacy of the Autoimmune Protocol Diet as a Part of a Multidisciplinary Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. Cureus, 11(4), e4556. https://pubmed.ncbi.nlm.nih.gov/31275780/
Krysiak, R., Kowalcze, K., Okopień, B., & Gdula-Dymek, A. (2023). Effects of an Autoimmune Protocol (AIP) Diet on Changes in Thyroid Parameters in Hashimoto’s Disease. Nutrients, 15(9), 2101. https://www.mdpi.com/2072-6643/15/9/2101













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