Why Your Thyroid Antibodies Aren’t Dropping

Welcome to Healthy Gut Healthy Thyroid!

This is your weekly roundup of the BEST actionable steps for those people with thyroid and autoimmune thyroid conditions who want to restore their health…by healing their gut. Whether you have hyperthyroidism or Hashimoto’s you will benefit from the content in this newsletter.

In today's issue:

• Main Topic: Why Your Thyroid Antibodies Aren’t Dropping

• Podcast Review: Can Peptides Help with Thyroid Conditions? | James Lavalle

• Ask Dr. Eric: Can Stored Trauma Be Preventing You From Healing?

Why Your Thyroid Antibodies Aren’t Dropping

Recently, a patient of mine with Graves’ disease received her latest thyroid panel. The results were somewhat mixed—her TSH, free T4, and free T3 were all within optimal ranges, yet her thyroid-stimulating immunoglobulins (TSI)—the autoimmune antibodies specific to Graves'—had increased.

This scenario isn’t uncommon, and it raises an important question I often hear: "Why are my antibodies going up even though I feel better and my labs look good?"

When this happens, my first step is to review whether the patient is truly implementing all the foundations of thyroid and immune healing:

✔️ Clean, anti-inflammatory diet (e.g., AIP or modified Paleo)

✔️ Stress management practices

✔️ Consistent, quality sleep

✔️ Regular—but not excessive—movement

In this particular case, she was doing everything “right.” Her diet was on point, she practiced daily stress reduction, and her sleep was solid.

So, what else could be going on?

Beyond Diet and Lifestyle Changes

In my book The Hyperthyroid Healing Diet, I include a section called "Beyond the Hyperthyroid Healing Diet", which underscores that while diet and lifestyle are foundational, they may not be enough for everyone.

It’s not uncommon for patients with hyperthyroidism or Hashimoto’s to have already made significant lifestyle changes before seeking my help. Many have cleaned up their diets, reduced stress, and prioritized sleep—yet their antibodies remain elevated.

That’s where personalized functional testing can provide missing pieces of the puzzle.

When Foundational Work Isn’t Enough

For many patients, additional underlying imbalances or hidden triggers are driving their autoimmunity. When I personally dealt with Graves’ disease, I didn’t stop at blood work—I also did an adrenal saliva test and a hair mineral analysis, which revealed key insights into my stress response and mineral imbalances.

The goal is to identify root causes, which may include:

✅ Adrenal dysfunction

✅ Gut dysbiosis or infections

✅ Mineral imbalances

✅ Environmental toxicants

✅ Mold exposure

✅ Food sensitivities

✅ Stealth infections (e.g., Epstein-Barr virus, Lyme disease)

A comprehensive health history helps determine which tests might be most useful. But admittedly, it’s not a perfect science.

The Challenges with Functional Medicine Testing

While I prefer testing over guessing, functional medicine tests have limitations:

False positives and false negatives can occur. For example, collecting a cortisol saliva test on an unusually stressful day may skew results, while a stool test might miss a parasite despite its presence.

No single test will uncover all your triggers. That’s why it’s often necessary to combine multiple tests or follow up with retesting if healing stalls.

Sometimes, the initial testing is enough. Other times, symptoms persist or antibody levels stay elevated, and further investigation is needed.

Retesting vs. Additional Testing

Returning to the patient I mentioned earlier, her antibody levels weren’t decreasing despite improvement in other markers. I had to decide: Should we retest previous systems (e.g., adrenals, gut), or order new functional tests that hadn’t yet been explored (e.g., organic acids test)?

Here’s how I usually decide:

If initial tests revealed major imbalances, it makes sense to retest and see if the protocols are working.

➜ If initial testing was inconclusive, I may recommend additional tests—such as a comprehensive stool panel, OAT (Organic Acids Test), or Cyrex Labs immune panels—to uncover overlooked imbalances or triggers.

➜ Every patient is unique, and progress isn’t always linear. The key is persistence and flexibility in your investigative approach.

Conclusion

If your thyroid antibodies aren’t decreasing, even though your diet is clean, stress is managed, and other lab markers look good—you’re not doing anything wrong.

You may simply need to dig deeper.

Autoimmunity is complex. It often takes a combination of:

• Incorporating the foundations of healing

• Functional medicine testing

• Targeted support

• Patience and persistence

Remember, improvement in symptoms and thyroid labs is encouraging—but elevated antibodies may indicate your immune system still sees a threat. Identifying and addressing that hidden threat may be the final piece to truly restoring immune balance.

Save My Thyroid Podcast Review

I have a podcast called "Save My Thyroid", where I discuss how people with hyperthyroidism and Hashimoto's can save their thyroid and regain their health. And during each edition of this newsletter I'll briefly discuss a recent podcast episode.

In a recent podcast episode I chatted with clinical pharmacist and author Jim LaValle about how specific peptides like BPC-157 and KPV can support gut health, reduce inflammation, and potentially accelerate healing in those with autoimmune thyroid conditions. He breaks down the mechanisms in layman’s terms, including how gut permeability and chronic stress can feed into conditions like Hashimoto’s and Graves’.

We also explore the nuances around GLP-1 medications for weight loss, the role of peptides in hair loss recovery, and whether certain compounds are appropriate for long-term use. Throughout, we return to the theme that peptides are tools—not magic—and they’re most effective when paired with foundational lifestyle shifts.

Click Here to learn where peptides can fit into your thyroid or autoimmune healing journey.

Ask Dr. Eric

During every issue I'll answer a question or two that I think can benefit most people with a thyroid or autoimmune thyroid condition. If you'd like for me to consider your question for a future edition of this newsletter email your question to [email protected].

QUESTION: CAN STORED TRAUMA BE PREVENTING YOU FROM HEALING?

Dr. Eric, I'm dealing with Hashimoto's and have hit a roadblock in my recovery, and I feel like I'm doing everything I can from a diet and lifestyle standpoint. I've also done quite a bit of functional medicine testing, and so I've been trying to figure out what is holding me back from getting better. I then listened to your interview with Dr. Aimie Apigian on stored trauma, and was wondering if this can be having a negative effect on my recovery?

Thanks for your question! There is no question that stored trauma can be a potential thyroid healing roadblock. In the past I had Dr. Aimie Apigian on my podcast, as she is an expert in this area. She feels that all autoimmune conditions are tied into trauma.

And while I question if this really is true, I have no doubt that past traumas are commonly overlooked, yet they can be the reason why someone doesn’t achieve optimal health.

Chronic Stress vs. Trauma

During my interview with Dr. Aimie she mentioned that most people aren't aware of the difference between chronic stress and trauma. She discussed how stress is a very high energy state, whereas the trauma response is a low energy state, and it feels like you don't have the energy to face the problem.

In other words, where the stress response is commonly described as a "fight or flight" response, when someone is in a trauma response they're done fighting. They don't have the energy to fight.

How To Address Stored Trauma

Dr. Aimie talks about somatic regulation skills, which refer to the ability to consciously control and manage physical sensations, bodily processes, and emotional responses, particularly in response to stress or trauma. It begins with noticing and becoming aware of how your body feels, and then using certain techniques to shift your physical and emotional state.

This can include breathwork and other types of mind body medicine techniques, but since trauma can dysregulate the nervous system, many times nervous system retraining can help. For more information on I would check out the Primal Trust and Gupta programs.

Additional Thyroid-Related Resources

Click Here for Can Peptides Help with Thyroid Conditions? (episode 206)

Click Here for Stored Trauma and Thyroid Autoimmunity (episode 69)

Click Here to access hundreds of thyroid-related articles and blog posts

Click Here to join the Graves’ disease and Hashimoto’s community

Click Here to purchase one of Dr. Eric’s thyroid-related books

Click Here to work with Dr. Eric and his team

That’s a wrap