The Hidden Causes of Chronic Symptoms: Autoimmunity, CIRS & What Your Labs Reveal
Chronic fatigue, joint pain, brain fog, and gut problems that come and go are not normal. They're often signs that something is keeping your immune system activated: autoimmunity, a thyroid problem, blood sugar swings, low cortisol, anemia, food sensitivities, or several of these at once. The right labs, read for patterns and not just red flags, can show what's really going on.
Key takeaways
- Autoimmune diagnoses are climbing fast, and they often start after hormone shifts, illness, big stress, or physical trauma.
- Symptoms that flare and fade in waves are a classic sign of immune dysregulation.
- Many women feel great during pregnancy, then crash after. There's a reason.
- A real thyroid panel is 7 tests, not just TSH.
- "Normal" labs can still hide patterns that point to the problem.
- Leaky gut often starts with slow cell turnover (like low thyroid), not a missing supplement.
Meet Dr. Stadler (again)
Dr. Stadler is back. He's the head physician for Dr. Josh Redd's Red River clinics and now leads Red River Orem (formerly Provo Health).
For years, I lumped my fatigue and brain fog into CIRS. Underneath it all, Dr. Stadler found thyroid problems that had been flying under the radar for about 12 years.
🎧 Listen to the full episode: The Hidden Causes of Chronic Symptoms
Why are so many people getting autoimmune diseases?
Dr. Stadler says autoimmune diagnoses have climbed sharply over the last 10 to 12 years. People are being diagnosed younger, and conditions that used to be rare (like antiphospholipid syndrome) now show up in his clinics about once a month.
The most common triggers he sees:
- Hormone shifts: puberty, pregnancy, and menopause
- Acute illness: COVID, a bad flu, or a lingering infection (like a UTI that turns into a kidney infection)
- Prolonged high stress
- Physical trauma: car accidents, sports or work injuries
These events can switch on genes that were sitting quietly, and the immune system doesn't switch back off.
Is it CIRS or something else?
The term CIRS is usually reserved for people who can't clear biotoxins, most often from water-damaged buildings. But lots of things drive chronic inflammation: autoimmunity, reactivated viruses, and food reactions you keep eating.
Dr. Stadler shared a patient who did a CIRS protocol, saw about 20 to 25% improvement, then stalled. More treatment. Over $100,000 in home remediation. Her doctor said there must still be mold. She ended up living in a tent in her backyard.
Her real issue? Two autoimmune conditions, one of which she'd been diagnosed with a decade earlier but never managed.
I know that rabbit hole. On Dr. Stadler's 1-to-10 autoimmune scale, I'm now a 4. I don't have to chase mold. I'm fine-tuning.
What symptoms shouldn't you ignore?
- Chronic fatigue: low energy 10+ days a month, or needing to lie back down after the school drop-off
- Body-wide joint, muscle, or tendon pain, especially if it comes in waves like you're getting sick but never do
- Brain fog: forgetting why you walked into a room, work performance slipping
- Gut symptoms: gas, bloating, pain, or bowel changes
- Headaches
- Weight changes that don't match your lifestyle
What's a normal bowel movement?
At least once a day, ideally twice. Look up the Bristol Stool Chart and aim for a soft, smooth "S." I was 23 before I learned that deer-pellet poops weren't normal.
Why do autoimmune symptoms come and go?
That ebb-and-flow pattern is one of the clearest signs of autoimmunity. You feel okay for a few days ("I could live like this"), then something triggers a flare that lasts 3 to 10 days.
Part of Dr. Stadler's work is teaching patients to spot their triggers, so a 10-day flare can become a 3-day flare.
This was a massive aha for me. So many of my "mold flares" were probably autoimmune flares.
Why do women feel better during pregnancy and worse after?
Pregnancy naturally dampens the immune system, almost like an immunosuppressive drug. For someone with autoimmunity, that can mean fewer flares.
Then comes birth. Dr. Stadler explains that a large volume of placental blood (with fetal proteins) gets pushed back into mom, which is a big immune activator. Add the physical trauma of birth, making breast milk, little sleep, and depleted nutrients. It's a perfect storm.
He also flagged postpartum thyroiditis. I was told I had Graves' after pregnancy, treated through the acute part, and assumed it was over. But if it weren't autoimmune, I wouldn't still have thyroid antibodies years later.
Do your symptoms come and go in waves? That's a clue worth following. 👉 Take the free Root Causes Quiz to see where your body is struggling most.
What labs should you ask for with chronic symptoms?
Dr. Stadler's baseline:
- CBC (complete blood count)
- Comprehensive metabolic panel
- Cholesterol panel
- A full thyroid panel (7 tests): TSH, T4, free T4, T3, reverse T3, T3 uptake, and thyroid antibodies (TPO and thyroglobulin)
- Inflammatory and autoimmune markers
From there, he casts a broad net for chronic inflammation, autoimmunity, infections, nutrient deficiencies, sex hormone and thyroid imbalances, blood sugar, stress hormones, and anemia. Then he goes deeper only where something shows up. He'd rather find the answer with $500 of testing than $2,500, unless the bigger panel is truly needed.
What does a morning cortisol test show?
Overnight, your body has to keep your blood sugar steady without food. It does that by making more and more cortisol through the night, which tells your liver to release stored sugar.
A morning cortisol shows whether your body can make that peak. Low morning cortisol helps explain waking up exhausted. It's often the first clue to bigger adrenal problems.
Can you have "normal" labs and still be sick?
Yes. Dr. Stadler looks for patterns across markers, not just numbers that cross a lab line.
His example: if your A1C is creeping up, he also checks your triglyceride-to-cholesterol ratio, chloride, carbon dioxide, and fasting glucose. When they all shift together, that tells a story, even if none are flagged "high" yet. He wants to catch a problem at 25% off, not 50%.
He also looks at albumin and globulin (blood proteins). Their ratio can shift with autoimmunity, a leaky gut, infection, and even POTS. Comparing my March and August labs, he could see when my gut was leaking more.
What really causes leaky gut?
Your gut lining replaces itself every 3 to 5 days. Thyroid hormone (T3) controls how fast cells regenerate. If your thyroid is off, that lining can't keep up.
So you can take every gut supplement out there, but if the thyroid issue isn't fixed, the gut leaks again within days of stopping. Supplements are support, not the fix.
Another surprise: overtraining can release zonulin and open up the gut lining within 24 hours.
Why do we react to gluten, dairy, and other foods?
Two different things happen:
- Inflammatory foods, like cane sugar, raise inflammation for almost everyone through insulin and blood sugar. That's not an immune reaction.
- True food sensitivities happen when the gut lining is leaky. Bigger protein fragments slip into the blood, your immune system mistakes them for invaders, and you make antibodies.
Why the usual suspects? Partly molecular mimicry. Pieces of gluten can resemble other proteins, including thyroid enzymes. And partly frequency. You react most to the foods you eat most, because those are what leak through.
For autoimmune patients, the most common reactive foods are gluten, dairy, eggs, soy, and tomatoes. But a mother and daughter with the same diagnosis may share only 20 to 30% of their trigger foods. That's why custom testing matters.
Are food sensitivity tests accurate?
Not all of them. Dr. Stadler's team once submitted the same blood under different names to test lab accuracy. Many companies returned completely different results. Ask your provider which lab they trust and why.
Frequently asked questions
What are early signs of autoimmune disease?
Ongoing fatigue, body-wide pain that comes in waves, brain fog, gut symptoms, headaches, and unexplained weight changes. Symptoms that flare and fade are a big clue.
What should a full thyroid panel include?
TSH, T4, free T4, T3, reverse T3, T3 uptake, and thyroid antibodies (TPO and thyroglobulin). TSH alone can miss a lot.
Can low thyroid cause leaky gut?
It can. Thyroid hormone controls how quickly the gut lining renews. When it's low, the lining may not repair fast enough.
Can pregnancy trigger autoimmune disease?
Yes. The immune shifts after birth, plus stress, sleep loss, and nutrient depletion, can trigger conditions like postpartum thyroiditis.
Where do you start?
You may have several mild problems adding up, not one big mystery. The key is finding them and fixing them in the right order.
That's what the Order of Healing™ maps out: 8 steps, from mindset and mitochondria through gut, liver, adrenals, thyroid, and sex hormones up to the brain.
👉 Download the free Order of Healing™ Guide and find your starting point.
🎧 Listen to the full episode on the Gutsy Health Podcast.
Want to work with Dr. Stadler? Call Red River Orem at 801-691-1765.
This post is for education only and isn't medical advice. Talk with a qualified provider before changing your treatment.
