AIP for Hashimoto’s: The Pioneering Abbott Pilot Study & Case Reports (Episode 61)

Hashimoto’s thyroiditis is the most common autoimmune disease in the world—and yet for many people, treatment still feels incomplete.

Even when thyroid labs fall within “normal” ranges, symptoms like fatigue, brain fog, pain, digestive issues, anxiety, and low mood often persist. For years, patients have been told that if their numbers look good, they should feel fine. But lived experience tells a different story.

In Episode 61 of the Autoimmune Wellness Podcast, I continue the AIP Medical Research Review series with a deep dive into the first clinical study ever conducted on the Autoimmune Protocol for Hashimoto’s thyroiditis. This pioneering, community-supported pilot study—led by Dr. Rob Abbott and published in 2019—helped bridge the gap between patient experience and clinical evidence.

This post expands on the episode and walks through the full story behind the study: how it began, how it was designed, what the intervention included, what changed (and what didn’t), and why this research still matters today for people living with Hashimoto’s.

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Watch the Episode

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The Conversation That Sparked the Study

In 2017, I met Dr. Rob Abbott, a family medicine physician who had read the first AIP pilot study for inflammatory bowel disease published by the Scripps team. In his own clinical practice, Dr. Abbott was seeing a growing number of women with autoimmune disease—particularly Hashimoto’s thyroiditis—who were struggling despite being “stable” on paper.

He shared that he had begun recommending the Autoimmune Protocol to some of his Hashimoto’s patients and was seeing consistent, meaningful improvements in symptoms. The changes were too significant to ignore.

That conversation sparked what became a true grassroots research effort. Through Autoimmune Wellness, Angie and I partnered with Dr. Abbott to help bring the study to life. The project was crowdfunded by the autoimmune community, recruited participants directly from that community, and was not backed by a university or pharmaceutical company.

Like the IBD pilot study before it, this research marked a turning point—when real-world healing stories were translated into measurable, peer-reviewed outcomes.

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Understanding Hashimoto’s Thyroiditis

Hashimoto’s thyroiditis occurs when the immune system mistakenly attacks the thyroid gland, gradually impairing its ability to produce thyroid hormone. Over time, this can lead to hypothyroidism.

Diagnosis typically involves thyroid hormone testing (TSH, Free T4, Free T3) and thyroid antibodies (TPO and thyroglobulin antibodies). But here’s the challenge: antibody levels and hormone values don’t always correlate with symptom severity.

Many people with Hashimoto’s are medically “euthyroid”—their hormone levels are within target ranges—yet still experience a high symptom burden. Thyroid hormone replacement is essential and often life-changing, but it does not directly address immune dysregulation, inflammation, gut health, nutrient status, or lifestyle factors that influence daily wellbeing.

This disconnect between labs and lived experience is exactly what the Abbott study set out to explore.

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Why Study AIP for Hashimoto’s?

Hashimoto’s is not only the most common autoimmune disease—it’s also one of the most common diagnoses among people who turn to AIP.

In Autoimmune Wellness surveys conducted in 2017–2018, more than half of respondents using AIP reported a Hashimoto’s diagnosis. Yet at the time, no clinical studies had examined whether AIP could support people with Hashimoto’s in a structured research setting.

The key question was simple, but powerful:

Can a comprehensive diet and lifestyle intervention improve symptoms, inflammation, and quality of life in Hashimoto’s patients who are already stable on medication?

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Who Participated in the Study

The pilot study enrolled 17 adults with Hashimoto’s thyroiditis, ages 20–45.

Important details about this group:

  • Participants were pre-menopausal and non-obese, to reduce confounding variables
  • All were euthyroid at baseline (labs within treatment targets)
  • None had previously used AIP
  • Despite “normal” labs, participants reported persistent symptoms

This is a population clinicians see every day: medically stable on paper, but still struggling in real life.

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What the AIP Intervention Included

The intervention was modeled after the earlier IBD pilot study and reflects what we now recognize as Core AIP.

Participants completed:

  • A 6-week staged transition (“SAD to AIP in SIX”)
  • Followed by a 4-week elimination phase
  • Emphasis on nutrient density (seafood, organ meats, vegetables, fermented foods, healthy fats)
  • Lifestyle practices including sleep, stress management, gentle movement, and time outdoors

Crucially, this was not a diet-only intervention.

Participants received:

  • Daily support from trained health coaches
  • Structured education and troubleshooting
  • A private online community
  • Guidance on meal planning, cooking, and lifestyle changes

This mirrors how AIP is practiced today and highlights the role of support and structure in successful implementation.

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How Outcomes Were Measured

Researchers used a combination of:

  • SF-36 (a validated quality-of-life survey)
  • Medical Symptom Questionnaire (MSQ)
  • Comprehensive thyroid labs and antibodies
  • hs-CRP (a marker of systemic inflammation)
  • Functional tests assessing gut health and nutrient status
  • All measures were taken before and after the 10-week intervention.

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Results: Quality of Life and Symptoms

The results were striking.

Participants saw statistically significant improvements across all eight domains of the SF-36, including:

  • Physical functioning
  • Energy and vitality
  • Mental health
  • General health perception

MSQ scores dropped dramatically, indicating broad reductions in symptom burden—less pain, better digestion, improved mood, clearer thinking, and more stable energy.

These improvements occurred in just 10 weeks.

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Results: Inflammation, Thyroid Labs, and Medication

Systemic inflammation (hs-CRP) dropped by 29%, moving participants closer to the low-risk range.

At the same time:

  • Thyroid hormone levels remained stable, by design
  • Thyroid antibodies showed only modest, non-significant changes

This matters.

It tells us that people can feel significantly better even when thyroid labs stay the same—a finding that validates what many Hashimoto’s patients report anecdotally.

Nearly half of participants on thyroid medication required dose reductions by the end of the study, while no one needed increased medication.

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Case Reports: Real-World Insight

One of the most unique aspects of this study was the inclusion of detailed narrative case reports for each participant.

These stories reveal the range of outcomes—from moderate improvement to dramatic transformation—and bring depth to the statistical results.

Participants described:

  • Resolution of long-standing pain or skin issues
  • Major improvements in sleep and resilience
  • Dramatic drops in symptom scores
  • Feeling “like themselves again” for the first time in years

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Why This Study is Important

This study remains a milestone because it showed that:

  • AIP can be safe, feasible, and effective for Hashimoto’s
  • Quality of life improvements can occur independent of lab changes
  • Structured support dramatically improves adherence and outcomes
  • Patient-centered care matters

Most importantly, it reframed what success in Hashimoto’s care can look like—not just better numbers, but better daily functioning.

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Practical Takeaways for Hashimoto’s Today

  • Improvements can happen quickly
  • Modified AIP may be a sustainable starting point
  • Track symptoms, not just labs
  • Lifestyle factors matter as much as food
  • Medication needs may change—monitor with your provider
  • Support makes the process safer and more sustainable

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AIP Foundation Series: Learn the Framework

If this episode sparked questions about how to apply AIP safely and effectively, the AIP Foundation Series is a great next step.

This free, 5-day email course includes:

  • Printable food lists
  • Core vs. Modified AIP guidance
  • Meal planning tools
  • Beginner-friendly education

👉 Sign up for the AIP Foundation Series

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The New Autoimmune Protocol (Coming Soon)

If you’re interested in the science behind AIP and how to apply it in real life, my upcoming book, The New Autoimmune Protocol, brings together:

  • Updated medical research
  • Clear guidance on Core and Modified AIP
  • New recipes and step-by-step meal plans

👉 Pre-order The New Autoimmune Protocol

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Listen to the Episode

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Episode Timeline

00:00 – The meeting that sparked the Hashimoto’s study
02:51 – Study overview
04:01 – Understanding Hashimoto’s
06:27 – Why AIP was studied
08:37 – Participant profile
10:09 – The AIP intervention
13:17 – Clinical measures
16:20 – Quality of life results
18:02 – Inflammation results
19:03 – Thyroid labs and antibodies
21:09 – Medication changes
23:29 – Case reports
26:02 – Why this matters
28:25 – Practical takeaways
32:16 – Wrap-up

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Episode Transcript

Below is the full transcript of Episode 61 of the Autoimmune Wellness Podcast.
This transcript is provided for accessibility and reference.

AIP For Hashimoto’s: The Pioneering Abbott Pilot Study & Case Reports (Ep 061)

[00:00:00] Introduction: The Meeting That Sparked a Study

In 2017, I was at a conference and had a conversation that quietly set the stage for a meaningful AIP research collaboration. I had just met a physician named Dr. Rob Abbott, who had read the first AIP pilot study for inflammatory bowel disease by the team at Scripps and wanted to talk about it.

In his family medicine practice, he had reported seeing a growing wave of women seeking care for autoimmune disease, especially this condition called Hashimoto’s thyroiditis, and this was far more than he expected early in his career. He told me that he had begun directing his Hashimoto’s patients to try the Autoimmune Protocol, and the results were consistent and compelling. Their symptoms improved in ways that were too significant to dismiss, and this got him interested in putting together a pilot study, this time using AIP for patients with Hashimoto’s.

Now, of course, when he shared this with me it immediately resonated and I got very excited. Not only was it a powerful clinical question, but this disease is personal for me as a Hashimoto’s patient myself. I know how common it is, how misunderstood it remains, and how often patients live with a high symptom burden, despite being successfully treated on paper.

So what followed was a true grassroots effort. Angie and I, through Autoimmune Wellness, worked side by side with Dr. Abbott to bring this study to life. We crowdfunded the project, and as a side note, thank you to every single person who donated back then, and our community helped recruit the participants. It should be noted that this study wasn’t backed by a university grant or a pharmaceutical company, but by patients, community members and practitioners who believed that it mattered.

And like the IBD pilot study before it, the Abbott Hashimoto’s study marked another turning point in AIP research, a moment when real world healing stories began transforming into measurable peer-reviewed results. Today we’re going to walk through the full story behind this study: the origin, the intervention, the results, the case reports, and how it set the stage for even more research using AIP for Hashimoto’s thyroiditis.

Welcome back to the Autoimmune Wellness Podcast. I’m your host, Mickey Trescott, and this is the second episode in our AIP Medical Research Review series where I walk you through the published clinical studies on the Autoimmune Protocol; what was examined, what was found, and what it all means for people living with autoimmune disease right now.

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.

[00:02:51] Episode Overview: The Abbott AIP Hashimoto’s Study

In today’s episode, we’re diving into the very first medical study conducted on the Autoimmune Protocol for Hashimoto’s Thyroiditis, a community-supported study published in 2019 by Dr. Rob Abbott and colleagues.

The name of the paper is: Efficacy of the Autoimmune Protocol Diet as a Part of a Multidisciplinary Supported Lifestyle Intervention for Hashimoto’s Thyroiditis, published in 2019.

If you would like to read along, you can find a direct link to the full open-access paper in the show notes.

We’re going to walk through the complete study design: who participated, what the AIP intervention looked like and how outcomes were measured. Then we’ll explore the results including improvements in symptoms, inflammation and quality of life, as well as some case reports that Dr. Abbott generously included to highlight some of the individual experiences.

By the end of this episode, you’ll have a clear understanding, not just of what happened in the study, but why it remains such an important milestone for Hashimoto’s patients and for the broader scientific recognition of AIP.

[00:04:01] Understanding Hashimoto’s Thyroiditis and Standard Treatment

To understand this study, we first need to talk about Hashimoto’s thyroiditis itself. Hashimoto’s is the most common autoimmune disease in the world. It occurs when the immune system mistakenly targets the thyroid gland gradually damaging the tissue responsible for producing thyroid hormones. Over time, this autoimmune activity can lead to hypothyroidism, which is a lack of thyroid hormone. The immune attack often begins years before hormone levels fall out of range and can continue even after medication brings those levels back to normal.

Diagnosis typically involves a combination of thyroid hormone tests and thyroid antibody markers. The thyroid hormones include TSH, which is thyroid stimulating hormone. This is the brain telling the thyroid what it needs to do. Free T4, which is the storage form of thyroid hormone and free T3, which is the active form that cells used for energy. And then the antibodies include TPO, which is thyroid peroxidase, and TG, which is thyroglobulin.

And elevated antibodies confirm the autoimmune nature of the condition, but they don’t always correlate with symptom severity. And this is where things get a little complicated. It’s also possible to be diagnosed with Hashimoto’s without these two antibodies being present based on imaging results on a thyroid ultrasound. So basically they look at the thyroid gland and can tell if there’s inflammation that’s consistent with Hashimoto’s. You can also get a diagnosis there.

Symptoms of Hashimoto’s are thought to stem from the resulting hypothyroidism, but sometimes they aren’t fully explained by the thyroid hormone levels alone. So fatigue, brain fog, anxiety, depression, digestive issues, hair loss, joint pain, menstrual changes, and depression are extremely common. And if that sounds like a big list, just remember that every cell in your body needs thyroid hormones. Quite literally, almost any type of symptom can be connected to hypothyroidism, if that is something that you are experiencing.

Thyroid hormone replacement is the standard treatment for Hashimoto’s, and in many cases it helps tremendously, but medication alone doesn’t address the ongoing autoimmune activity, nor the inflammation, the nutrient issues, the gut dysfunction, or the lifestyle factors that contribute to persistent symptoms.

[00:06:27] Why Study AIP for Hashimoto’s Thyroiditis?

So why study AIP for Hashimoto’s thyroiditis? Hashimoto’s is not only the most common autoimmune disease, it’s also one of the most represented conditions in the AIP community. We surveyed in 2017 and 2018 through the Autoimmune Wellness channel, more than 3,000 people with autoimmune disease who had used AIP, and over half of them reported turning to the protocol because of a Hashimoto’s diagnosis.

While thyroid hormone replacement is essential and often very effective, it addresses only one part of the condition, the deficiency in thyroid hormone. It doesn’t address the ongoing autoimmune activity that drives inflammation or the fatigue, the brain fog, the digestive issues, the mood symptoms, and the pain that many people continue to experience even when their labs look normal on paper.

And this disconnect between lab values and daily lived experience is something that many patients know well. I experienced it myself when I was diagnosed with Hashimoto’s at 26 years old. I was struggling with significant symptoms despite being told that my thyroid numbers were fine, and my story is just one example of a pattern that is widely reported across the Hashimoto’s community.

And because of this gap, many patients seek out additional tools to support their health. And AIP is one of the more common approaches that they turn to often because they’re looking for a structured way to improve their health. And clinicians, including Dr. Abbott, we’re seeing these patterns too. So until this study, those experiences had not been documented in a clinical setting.

Studying AIP for Hashimoto’s offered an opportunity to explore an important question. Can a structured diet and lifestyle intervention provide measurable support for patients who are stable on paper but still struggling in real life? This research aimed to bring clarity to that question and begin filling the gap between conventional thyroid treatment and the persistent symptoms that so many of us live with every day.

[00:08:37] Study Participant Profile

With that background, let’s dive into the study itself and start with the participant profile. This pilot study enrolled 17 adults with Hashimoto’s thyroiditis all between the ages of 20 and 45. These were not individuals with uncontrolled thyroid labs or multiple complicating conditions. In fact, the researchers intentionally selected pre-menopausal, non-obese adults to minimize hormonal variability and reduce confounding factors related to metabolic disease or rapid weight changes.

And here’s an important detail. These participants were euthyroid, meaning their thyroid hormone levels were within normal treatment targets at baseline. They were not newly diagnosed, wildly unstable, or in need of medication adjustments. On paper, their thyroid function looked fine, yet they were still experiencing the persistent symptoms that so many Hashimoto’s patients report.

The researchers also excluded anyone who had used AIP in the past. They were encountering the protocol as a new intervention, just like the participants in the IBD pilot study. So the group enrolled here represents a realistic and commonly seen subset of the Hashimoto’s population: living with ongoing symptoms, medically stable on paper, and looking for tools beyond that medical support to support their wellbeing. This is the exact population many clinicians struggle to support.

[00:10:09] The AIP Study Intervention

Next, let’s talk about how the AIP intervention was structured in this pilot study. This one was modeled after the intervention in the AIP IBD pilot study that came before it with a little adjustment on timing to accommodate some of the testing.

Just like in the IBD study. The intervention was intentional, phased, and highly supported. In this study, participants completed the same six week staged elimination process. Instead of removing every food group at once, they followed a weekly sequence of eliminations, additions, and lifestyle practices to help them adjust gradually and safely. This six week transition was then followed by a four week maintenance phase. As with the IBD study, what the researchers called the maintenance phase is actually what we know of in the AIP community as the elimination phase.

This means that the total intervention lasted 10 weeks, six weeks for transition and four weeks for elimination, which is actually relatively short. The elimination phase used in the study aligns with what we now call Core AIP, and removes all grains, legumes, nightshades, dairy, eggs, alcohol, nuts and seeds, food additives.

And then alongside those eliminations, the program emphasized the AIP Foundation of nutrient density. Participants were encouraged to eat organ meats, seafood, bone broth, fermented vegetables, healthy fats, and a wide variety of fruits and vegetables.

And just like the IBD study, the intervention was not just limited to food. Participants also worked on lifestyle practices that support immune regulation and healing. These include sleep and sleep hygiene, stress management, gentle movement, building their support systems, and increasing time outside.

This is reflective of AIP as a holistic framework, not just a dietary pattern, which is exactly how it’s practiced and taught today. And I think that this is a point that gets easily lost when we talk about the results, so remember that the intervention here did not just focus on eliminations, but also adding nutrient-dense foods as well as making those lifestyle changes too.

Another core piece of the intervention was the support structure. Participants were supported by health coaches who provided daily guidance, a virtual group setting with a private community, email access for questions and structured educational content on eliminations, additions, and lifestyle changes.

They also got some help with menu planning, shopping tips, cooking guidance, and recipes, which was really facilitated by the health coaches who led daily discussions, answered questions, and encouraged participants through challenges and helped them troubleshoot when issues came up.

This coaching model is exactly what we teach in the AIP Certified Coach program, that a structured, supportive and education-based approach helps individuals implement AIP accurately, safely, and in a way that respects both their symptoms and their capacity.

[00:13:17] Clinical Measures & Assessments

Next, let’s talk about the clinical measures the researchers used. In this study the research team used a combination of questionnaires, comprehensive blood work, and functional medicine testing to assess both symptom changes and physiological changes. During the two week washout period before the intervention began, participants completed a detailed baseline assessment. This included several tools.

First, the 36 item short form health survey. This is known as SF-36, is a widely used and validated survey tool that measures social, emotional and physical wellbeing. It looks at things like physical functioning, energy levels, emotional health, pain, social participation. Higher scores indicate a better quality of life.

Next, they used a medical symptoms questionnaire or MSQ used frequently in functional medicine that evaluates symptom burden across multiple body systems, including digestion, mood, energy, and pain. This questionnaire isn’t validated or used often in research, but provides a detailed picture of symptom burden.

Next, the NIH Food frequency questionnaire was used to provide a detailed snapshot of dietary patterns at baseline. After completing all of these questionnaires, participants provided fasting blood samples to evaluate a broad range of biomarkers. These included a thyroid hormone panel, which included TSH, free T4, free T3, total, T4, total T3, and reverse T3.

They also tested thyroid antibodies to assess autoimmune activity, which included thyroid peroxidase antibodies, thyroglobulin antibodies, and they also included hs-CRP as a marker of systemic inflammation.

Lastly, they also included a complete blood count, CBC, and a comprehensive metabolic panel, CMP, to evaluate immune cell counts, liver and kidney function, blood glucose, electrolytes, and overall metabolic status. This helps ensure participant safety and provides a broader context for the physiological changes.

And then lastly, through a partnership with Genova Diagnostics, participants also completed: an organic acid test, which offers insights into nutrient status, detoxification and gut microbiome metabolites, and a GI effects stool analysis, which evaluates digestive function, gut inflammation and microbial balance.

While these tests are not always included in conventional research, they can give additional information about gut health and metabolic function. And all of these assessments, the lab work, the questionnaires, the functional tests, were repeated at the end of the 10 week intervention. This allowed the researchers to compare the baseline status with post intervention results and determine whether meaningful changes occurred.

[00:16:20] Results – Quality of Life

Let’s move on to discussing the results and start with the outcomes that matter most to people living with Hashimoto’s: quality of life and daily symptoms. In this study, both improved in ways that were not only noticeable, but statistically significant. The SF-36 is a validated tool that measures eight domains of wellbeing from physical functioning to energy levels to emotional health.

In this trial, scores improved across all eight subscales, which is remarkable for a 10 week intervention. Some of the biggest changes were seen in physical role functioning, which pre-intervention median was 25, post was 100. Vitality, which is basically energy levels. Pre-intervention, median was 23, post-intervention was 58. General health perception, which pre-intervention was 40, post was 70. And improvements were also seen in mental health with median scores increasing from 54 to 78, which is a 22 point change. So taken together these numbers paint a clear picture– participants felt better physically, mentally, and emotionally in ways that were both measurable and meaningful.

Next, the medical symptom questionnaire looks at symptoms across multiple areas: digestion, mood, pain, energy, and more. Higher scores mean more symptoms. And in this study, MSQ scores dropped significantly indicating a broad reduction in symptom burden. Participants reported fewer digestive issues, more stable moods, clearer thinking, better energy, less pain and discomfort.

[00:18:02] Results – Inflammation and hs-CRP

The next outcome the researchers looked at was systemic inflammation measured by high sensitivity, C-reactive protein, or hs-CRP. This marker doesn’t tell us where inflammation is happening, but it gives a clear picture of whether overall inflammatory activity is rising or falling. In this study, hs-CRP levels decreased significantly over the 10 week intervention. Among the 14 participants with complete data, hs-CRP dropped by 29% from an average of 1.63 mg/L to 1.15 mg/L.

This reduction is meaningful, especially considering that participant’s thyroid hormone levels remained stable throughout the study. We’re going to talk about that next. This decrease in hs-CRP suggests that the body was experiencing less inflammatory stress, which aligns with the significant improvements participants reported in their energy, their mood, and their overall wellbeing.

[00:19:03] Results – Thyroid Hormones and Antibodies

Now let’s look at the thyroid labs, both hormones and antibodies, because these results help us understand what was driving the improvements that the participants experienced. In this study, thyroid hormone levels remained stable throughout the 10 week intervention, and that was intentional. Dr. Abbott monitored the participant’s thyroid labs and adjusted medication as needed to keep TSH, free T4, and free T3 within their target ranges.

This ensured that any improvements in symptoms or inflammation could not be attributed to shifts in thyroid hormone dosing. And that’s exactly what happened, TSH free T4, free T3, total hormones and reverse T3 showed no significant changes from baseline. This stability is important because it tells us the improvements in quality of life, symptom burden, and inflammation were not likely due to the result of changes in thyroid function or in medication. They were more likely the result of the AIP diet and lifestyle intervention itself.

The study also measured TPO antibodies and thyroglobulin antibodies, which reflect autoimmune activity against the thyroid. These antibodies showed a very slight downward trend, but the changes were not statistically significant over that 10 week period, which isn’t really surprising given the size of the group and the timeframe.

And here’s an important nuance. While some clinicians aim to reduce thyroid antibodies as a treatment target, antibody levels don’t always correlate with symptom burden, and they’re not a reliable marker for how someone feels. Participants felt significantly better, inflammation decreased, quality of life improved across all of those SF-36 domains, even though antibodies did not change dramatically at all.

So this points to a possibility. Maybe somebody can experience meaningful improvements in Hashimoto’s symptoms and overall wellbeing even when thyroid labs stay the same. And this is a pattern that many patients report anecdotally in real life. And the study helps validate that in a clinical setting.

[00:21:09] Results – Thyroid Medication Use

Another noteworthy outcome from the study was the pattern observed in thyroid medication use. While the goal of the trial was to keep thyroid hormone levels stable, several participants ended up needing less medication by the end of the 10 weeks.

Here’s what the study found. Six out of the 13 participants, so 46%, who started the trial on thyroid hormone replacement, decreased their dose during the study. . Three participants had already been asked to reduce or alter their medication type before the intervention began because their baseline labs showed that their TSH was too low or their other free hormones were too high. After that 10 weeks, all three of those participants required additional dose decreases.

And then another three participants lowered their medication dose after the intervention based on those post study labs. And then lastly, all three participants, I know this is a lot of groups of three, the three that entered the study without taking any thyroid hormone, were able to remain off medication entirely through the end of the trial.

This was not a formal endpoint of the study, and the trial was definitely not designed to test whether AIP reduces medication needs. But it is very interesting to see a trend for reduced medication use, especially since none of the participants needed more medication during or after the study.

[00:22:36] Results – Adherence and Safety

Before we move on, it’s important to highlight how participants tolerated the intervention, because feasibility and safety are key parts of evaluating any therapeutic approach. In this study, adherence to the AIP protocol was exceptionally high, with food frequency reviews showing a 95% adherence across the 10 week program.

There were no moderate or severe adverse effects reported. A few participants noted that the early stages of elimination were mentally challenging something that is very common when changing long established eating patterns, but that these challenges were quickly outweighed by improvements in symptom burden, energy, mood, and overall quality of life.

Taken together these findings show that a structured, coached AIP program is both safe and feasible, even for individuals living with ongoing symptoms of autoimmune thyroid disease.

[00:23:29] Case Reports: A Look Inside Individual Results

Now before we wrap up the results, I want to highlight something very unique about this study. In addition to reporting group averages and statistical outcomes, Dr. Abbott and his team included detailed narrative case reports for each participant. Something that we rarely see in nutrition intervention research.

These case reports are incredibly generous because they give us a window into the lived experience of those individual participants, how they were feeling at the start, what symptoms were most disruptive, how their labs looked, what changed during the intervention, and how their quality of life shifted by the end.

And for anyone living with Hashimoto’s, these stories help translate the data into real life context. They show the true range of what’s possible from moderate improvements to truly dramatic transformations, and they highlight the magnitude of change that can sometimes be lost when we only look at the big group as a whole.

Here are just a few of the most compelling individual outcomes from the case report section. One participant entered the study with a severe symptom burden affecting nearly every system: headaches, joint pain, digestive distress, fatigue, mood swings, and more. After 10 weeks on AIP, her MSQ score dropped from 103 to 36. She lost 10 pounds, her sleep and energy improved, and she described a profound shift in daily functioning.

Another participant’s story was especially striking. She began the study with an MSQ of 89, along with anxiety, joint pain, mood symptoms, and GI issues. By the end of the program, her symptom score fell to six, one of the most dramatic improvements in the entire trial, and her hs-CRP dropped from 2.42 to 0.84, signaling much lower inflammation. She described feeling calmer, clearer, and much more energetic.

A woman with a long history of skin issues and joint pain saw her MSQ improve from 83 to 25, with a complete resolution of eczema and joint symptoms. Her energy, sleep and mood also improved and she experienced greater resilience during life stressors, despite her thyroid labs remaining completely stable.

So this is just a summary of a few of the case reports, but they offer a powerful compliment to the statistical results, and I’d encourage you to give them a read if you would like to learn even more.

[00:26:02] Discussion & Why This Matters

So now that we’ve covered the results, let’s talk about why this pilot study still matters for people with Hashimoto’s today. First, this was the very first trial to test AIP for Hashimoto’s, and it validated what patients had been reporting for years. Even with stable thyroid labs and antibody levels, participants experienced major improvements in fatigue, pain, mood, brain fog, digestion, and overall quality of life. In fact, the gains across SF-36, vitality, mental health, general health and physical functioning were far larger than what’s been observed in medication only studies, and they happened in just 10 weeks.

Second, the study showed that symptom relief isn’t always tied to changes in thyroid hormones. Labs stayed stable, but inflammation didn’t. Hs-CRP dropped into the low risk range, and immune markers shifted in ways that suggest real modulation of the autoimmune process. This reinforces something fundamental for Hashimoto’s: healing is not just about those lab values, it’s about how you feel and how you function day to day.

And third, nearly half of the participants on thyroid medication actually needed lower doses by the end of the study. This is a remarkable finding. It suggests improved tissue sensitivity to thyroid hormone as inflammation and overall health improved.

And fourth, the study demonstrated that AIP can be safe, effective, and highly doable with the right support. That high adherence was largely because the intervention was not just a diet. Participants had coaching, community, gradual eliminations and steady guidance, and this mirrors what we see across AIP today. Structure and support dramatically improve outcomes.

Finally, this study broadened what’s possible in Hashimoto’s care. It showed that a comprehensive nutrition and lifestyle approach can meaningfully transform quality of life even when medication alone can’t, and helped pave the way for future AIP and lifestyle based thyroid research.

In short, this early trial demonstraed something powerful: your symptoms, energy and wellbeing can improve dramatically even when your labs stay the same. And that insight continues to shape patient-centered Hashimoto’s care today.

[00:28:25] Practical Takeaways for Listeners

What does all of this mean if you are considering using AIP to support Hashimoto’s today? Across this pilot study and what we now understand from years of AIP practice, several key themes emerge.

First, improvements can happen quickly, often within the first month. Many participants reported noticeable changes in energy, mood, pain, and digestion, with only four weeks in the elimination phase, which is that bare minimum that we recommend.

Number two, AIP can be safe and effective when implemented in a structured way. So here participants maintained 95% adherence and experienced no serious adverse events throughout the 10 week protocol. The study used a clear phased structure with gradual eliminations in a defined framework, and that structure played a major role in making the intervention both safe and doable. Following a clear plan rather than improvising or restricting at random is key to experiencing steady progress without unnecessary stress.

Three, look for improvements in quality of life, not just your thyroid hormones. Thyroid hormone levels and antibodies stayed relatively stable here, yet quality of life shifted dramatically. Participants reported more energy, reduced pain, improved mood, greater day-to-day capacity. So for many people with Hashimoto’s, symptoms don’t always match those lab values. So make sure that you are tracking well to assess how your symptoms are changing over time.

Number four, nutrient density and lifestyle changes are a part of success. So this is not a diet only intervention. Participants improved because they also worked on nutrient rich eating, sleep, and circadian rhythms, stress management practices, movement, connection, and community. Now, this is not to make AIP super overwhelming, but you should definitely know that these pillars directly impact inflammation, immune balance, and energy levels, and they’re not extras. They are essentials. So make sure that you’re implementing some small changes in all of these areas.

Number five, Modified AIP might be an excellent starting point. So participants in the study followed Core AIP, and they still experienced rapid improvement. But today we know that many people can achieve meaningful results beginning with Modified AIP. It keeps the nutrient density and lifestyle foundation intact while easing some of those eliminations, making the process more sustainable. So if you’re considering starting soon, I definitely recommend Modified AIP.

Number six, your medication needs might shift. So stay in touch with your provider. Get tested often. Nearly half of the participants who were taking thyroid medication, needing less of it by the end of this study. So AIP absolutely does not replace medication, but reducing inflammation and improving overall health can change how your body uses thyroid hormone. If you are starting AIP, work with your provider to monitor your symptoms and labs so that your dosing stays appropriate.

Number seven, support makes the journey easier, clearer, and more sustainable. These participants thrived with coaching, community accountability, and ongoing education. So whether that is working with an AIP Certified Coach, a functional medicine practitioner, or just being in a supportive online group, you do not have to do this alone. And support often determines how smooth that process feels.

So taken together, this study showed that something powerful is possible. Your symptoms, your energy, mood, and quality of life can improve dramatically even if your thyroid labs don’t change. And for anyone who’s living with Hashimoto’s who still doesn’t feel well, despite those quote unquote normal labs, this study offers hope and a clear framework for what to do next.

[00:32:16] Recap and Wrap-Up

Let’s quickly recap what we covered today. We talked about who was studied: those 17 adults with Hashimoto’s who were medically stable on paper, yet still struggling with significant symptoms, a group that reflects a large portion of the Hashimoto’s community.

We reviewed what changed: across just 10 weeks of using AIP, participants saw meaningful improvements in quality of life, symptom burden, inflammation, and even some nutrient markers. All while thyroid hormone levels were intentionally kept stable. Nearly half of those on thyroid medication needed slightly lower doses by the end of the study.

And we explored why this matters: this trial showed that AIP can be safe, feasible, and supportive for people with Hashimoto’s, validating what many patients experience anecdotally and paving the way for more research on thyroid autoimmunity.

I want to thank the participants who shared their time and their stories, and the Autoimmune Wellness community and donors whose generosity made the study possible. This research exists because you believe that it mattered.

If you enjoyed this episode, please subscribe so that you don’t miss the rest of the medical research review series. Ratings, reviews, and comments on your favorite platform are a huge help in getting this information to more people.

And finally, if you want to continue learning, download my AIP Foundation Series at theautoimmuneprotocol.com/foundations. It’s a free, five day email course with over 60 pages of resources and guides. Once you are all signed up, you will also receive an email anytime a new AIP study is published with my breakdown, so you can stay up to date with the research as it evolves.

And if today’s episode got you excited about the science, you are going to love my forthcoming book, The New Autoimmune Protocol, releasing this May. It brings together all of the updated medical research on AIP, plus completely new recipes for both Core and Modified AIP, and step-by-step meal plans so that you can put science into practice. You can pre-order your copy now and it truly helps get this work into the hands of more people who need it.

Thank you so much for joining me for this episode in the AIP Medical Research Review series. I’ll see you next time.

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Reference

Abbott, R. D., Sadowski, A., & Alt, A. G. (2019). Efficacy of the Autoimmune Protocol Diet as Part of a Multidisciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. Cureus, 11(4), e4556. https://doi.org/10.7759/cureus.4556

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About Mickey Trescott, MSc.

Mickey Trescott is a founder of Autoimmune Wellness, the host of The Autoimmune Wellness Podcast, and a co-creator and lead educator of AIP Certified Coach. She has been a leader in the Autoimmune Protocol (AIP) movement since its earliest days and has worked as a health coach since 2013. After recovering from a severe autoimmune health crisis following diagnoses of celiac disease and Hashimoto’s thyroiditis (and later psoriatic arthritis), Mickey began creating practical, accessible AIP resources to help others navigate autoimmune disease with clarity and confidence. She holds a Master’s degree in Human Nutrition and Functional Medicine and has contributed to the development and communication of AIP medical research. Mickey is the author of several best-selling books, including The Autoimmune Paleo Cookbook, The Autoimmune Wellness Handbook, The Nutrient-Dense Kitchen, and The New Autoimmune Protocol. You can find her sharing recipes and cooking demos on Instagram.

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