The Short Answer

Autoimmune conditions share a common root cause—immune system dysregulation—which means having one autoimmune disease significantly increases your risk of developing others. The good news: functional medicine management of your current autoimmune condition, whether it’s Hashimoto’s low thyroid or another autoimmune disorder, can substantially lower that risk by addressing the underlying immune imbalance.

“I had several autoimmune diseases and was going to different doctors, but couldn’t find anyone to help me feel like I used to before I got sick. I would have maybe four good days a month. Now I have 28 or more good days a month with functional medicine management.” — Anonymous, patient from RedRiver Health and Wellness Center

Why Autoimmune Diseases Cluster Together

Autoimmunity stems from an immune system that has become overzealous and imbalanced. Once you develop one autoimmune disease, you’re at increased risk for developing more. You may even already have another autoimmune reaction happening, it’s just not advanced enough to produce symptoms yet.

At RedRiver, we’ve observed this pattern firsthand. When we tested 100 patients with Hashimoto’s low thyroid for other autoimmune reactions, 50 percent came back positive for myelin basic protein antibodies, the marker for multiple sclerosis. This is a powerful example of why managing your current autoimmune condition is so important for preventing the development of additional autoimmune diseases.

A 2012 study showed that about one in six people with autoimmune conditions has another autoimmune disease. The most common combinations include:

Atrophic gastritis (chronic stomach inflammation causing pain, nausea, vomiting, and ulcers)

Vitiligo (loss of skin color and development of white patches across the body)

Celiac disease (reaction to gluten that can cause severe gastric, brain, or skin reactions)

Antiphospholipid syndrome (can cause blood clots, miscarriages, or stillbirths)

Multiple sclerosis (gradual loss of nerve sheaths causing vision loss, pain, fatigue, and impaired coordination)

Patients with multiple autoimmune conditions also commonly exhibit chronic unexplained anemia and recurring pregnancy losses.

Detecting Autoimmune Disease Before Symptoms Progress

Many people have undiagnosed autoimmune conditions because conventional lab tests appear normal. This makes prevention and early management difficult. If you experience symptoms like weight gain, cold hands and feet, depression, fatigue, and hair loss, you may need a thorough functional medicine evaluation.

If you suspect an autoimmune condition, testing should go beyond standard screening. For example, if you suspect Hashimoto’s low thyroid, you need more than just thyroid-stimulating hormone (TSH). Request testing for TPO and TGB antibodies:

TPO (thyroid peroxidase) is an enzyme in the thyroid gland that plays an important role in thyroid hormone production

TGB (thyroglobulin) is a protein made by the thyroid gland

When your immune system attacks either of these, it produces antibodies that can be detected on a blood test. The presence of these antibodies signals that your immune system is dysregulated and that other body tissues are susceptible to autoimmune attack.

The Gluten Connection in Autoimmune Disease

Most patients with autoimmune diseases respond very well to a strict gluten-free diet. Gluten triggers a strong inflammatory reaction in many people, eventually causing intolerance. Because portions of the gluten protein share the same molecular structure as tissue in various parts of the body, consuming gluten can trigger immune attacks against those tissues.

Research shows a direct connection between gluten and numerous autoimmune diseases. If you have undiagnosed gluten intolerance, eating gluten regularly keeps your immune system in a constant hypervigilant state. This causes chronic inflammation, exacerbates autoimmune symptoms, and increases your risk of developing additional autoimmune diseases.

The Autoimmune Paleo (AIP) Diet for Deeper Healing

Some autoimmune patients improve significantly on a gluten-free diet alone. Most, however, need to follow the autoimmune paleo (AIP) diet to identify other foods triggering inflammation and autoimmune symptoms.

Many people with autoimmune conditions develop multiple food sensitivities due to intestinal permeability, or “leaky gut,” a condition in which the gut walls become damaged and overly porous. This allows undigested foods, bacteria, and pathogens into the bloodstream, triggering inflammation, food sensitivities, and autoimmune flares.

Addressing leaky gut is foundational to most autoimmune protocols. One of the first steps is following the AIP diet, which eliminates foods that commonly provoke immune reactions, for at least four to six weeks. Many patients also benefit from eliminating dairy, corn, or other grains. In addition to dietary changes, select nutritional and herbal compounds have been shown to help restore the gut lining.

Sometimes dietary changes alone can substantially reduce autoimmune flare-ups and slow the progression of tissue damage.

The Three Key Hormonal Imbalances Driving Autoimmune Flares

In our practice, we identify three interconnected factors that often substantially drive up inflammation and autoimmune flares:

Cortisol: This adrenal hormone governs your stress response. Autoimmune patients often have chronically high or low cortisol levels, which can fuel inflammation.

Insulin: This hormone regulates blood sugar. Many autoimmune patients have chronically high insulin, a precursor to diabetes, creating a highly inflammatory state throughout the body and brain.

Estrogen: The majority of autoimmune patients are women, and estrogen imbalances are common in this population. Cortisol and insulin imbalances drive hormonal imbalances, particularly with estrogen, which amplifies inflammation. Men can also be affected by estrogen imbalances, which can sometimes lead to the development of female characteristics.

These three imbalances work together to keep the body chronically inflamed and to prevent its ability to restore and repair damaged tissue, especially the intestinal lining. This damaged lining, or intestinal permeability, allows undigested foods, bacteria, yeast, and pathogens to escape into the bloodstream, triggering widespread immune responses and inflammation.

By addressing these three areas of dysfunction, functional medicine can help restore gut wall health, lower systemic inflammation, and reduce autoimmune attacks against tissues. This approach also dramatically improves brain health, which is extremely vulnerable to inflammation and these hormonal imbalances. Better brain function enables improved communication between your brain, organs, and immune system for optimal function.

Going Beyond Diet: Advanced Functional Medicine Strategies

Sometimes diet alone isn’t sufficient, and more intensive therapy is warranted. Advanced approaches include:

Identifying and addressing viral, bacterial, or fungal infections

Addressing chemical sensitivities

Restoring the gut microbiome (colonies of healthy bacteria in the digestive tract)

Addressing liver health

Identifying additional factors triggering autoimmune attacks