Understanding the Gluten-Autoimmunity Connection

If you’ve been to a restaurant in the last few years, you’ve likely noticed a pattern: someone’s asking for the gluten-free menu. Maybe it’s you. Maybe it’s your neighbor, your niece, or your coworker. To support the growing number of people interested, available products to support gluten-free eating are popping up everywhere and grocery store shelves are filled with options. But what’s going on? Why does it seem like everyone is suddenly sensitive to gluten?

Part of the answer lies in how our food has changed. Wheat today is not the wheat of our grandparents. It’s been hybridized to increase yield and gluten content, treated with chemicals to manage large-scale production,, and it's often processed in ways that strip it of nutrients and fiber. Many gluten-containing foods are also ultra-processed, filled with preservatives and chemicals that further burden digestion. Add in widespread gut dysfunction, increased stress, poor sleep, and the overuse of antibiotics, and it’s no surprise that more bodies are saying, “I can’t handle this.”

Let’s focus on just the gluten piece of the puzzle and unpack what’s actually happening—because this isn’t just a trend. It’s a clue.

What Is Gluten?

Gluten is a protein found in wheat, barley, and rye and related grains. It’s what gives dough its elasticity and that satisfying chew. Without it, your bread would be flat and crumbly. Even among different types of wheat, gluten content can vary. Many home bakers discover that 100% whole wheat dough doesn’t rise well unless they add some high-gluten white flour to support the structure. Clearly, gluten plays an important role in baking. But what role does it play in your body?

Digestion is a complex symphony of enzymes breaking down food into smaller, absorbable parts. Carbohydrate digestion starts in the mouth, but protein digestion begins in the stomach and continues into the small intestine. Gluten, like all proteins, is made up of amino acids that can be thought of as beads on a pearl necklace. Your digestive enzymes are supposed to snip the necklace into individual beads so they can be absorbed and used by your body.

But gluten doesn’t break down easily into individual amino acids. This leaves large protein fragments, or peptides, that aren’t absorbable or usable. Instead, they linger in the gut, where they can cause trouble.

When the Immune System Gets Involved

Your gut isn't just a digestive organ; it's also home to around 70% of your immune system. That’s no coincidence. Your immune system is constantly surveilling your digestive tract to determine what’s friend and what’s foe. When it encounters these undigested gluten peptides, it may interpret them as a threat and mount a response in an attempt to keep you safe.

One response is with increased inflammation. The lining of your gut, which is supposed to act like a tight-knit barrier, begins to open up. This is what’s known as “leaky gut,” or intestinal permeability. And once the gut lining becomes permeable, those gluten fragments (and other things that shouldn’t be in your bloodstream) can slip through. Once these larger molecules enter the blood, the immune system continues its defense by launching a full-body inflammatory response. Increased gut permeability can let in more than just these large gluten fragments, and some develop reactions to other foods because they too slip by the body’s natural barrier to molecules that haven’t been properly broken down to size–never attributing the reaction to gluten’s role.

In some people, the immune system even starts attacking the body’s own tissues because gluten peptides can also mimic human proteins, a phenomenon called molecular mimicry. If a gluten fragment looks similar to a piece of your thyroid, brain, or joints, your immune system might get confused and go after both. This is one of the ways gluten can contribute to autoimmune disease.

Gluten and Autoimmunity

Even if you don’t have a diagnosed autoimmune condition, gluten-related inflammation can still cause widespread symptoms and interfere with your quality of life. But for those with autoimmune disease, gluten may not just be an irritant, it could be a trigger.

Celiac disease is the most well-known condition tied to gluten, where the immune system directly attacks the small intestine in response to gluten ingestion. But research now links gluten sensitivity to a growing number of other autoimmune conditions like Hashimoto’s thyroiditis, type 1 diabetes, psoriasis, rheumatoid arthritis, lupus, multiple sclerosis, and more.

What’s more surprising is how many people experience symptoms without having celiac disease. An estimated 1 in 3 people who react to gluten test negative for celiac. Their condition is called Non-Celiac Gluten Sensitivity (NCGS), and it typically flies under the radar of conventional medicine. These people, when they test for Celiac disease, come back negative.

What Is Non-Celiac Gluten Sensitivity?

Unlike an allergy or autoimmune response, NCGS is usually a slower, less dramatic immune reaction, often mediated by a different arm of the immune system (IgG rather than IgE). But the symptoms can be significant: bloating, cramping, fatigue, joint pain, headaches, brain fog, cravings, mood issues, and more. One of the most confusing parts is that symptoms may not show up right after eating gluten. You might feel fine after your sandwich today and struggle to focus or sleep tomorrow, never realizing the two are connected.

For others the association between the two is more immediate, yet we’re hesitant to make the connection. For years, I brushed off bloating and gut discomfort as “just the way my body works.” It wasn’t until I removed gluten completely that I realized how much better I felt when the gut pain went away. What I thought was “normal” was actually an inflammatory response. My body had been trying to get my attention, I just hadn’t known what to look for.

You Don’t Need a Diagnosis to Experiment

One of the most empowering aspects of Functional Nutrition is that you don’t need a diagnosis to start healing. You can begin with curiosity. If you suspect gluten might be contributing to your symptoms, try eliminating it completely for 30 days. Not just reducing it, but removing it entirely. That includes not just obvious sources like breads and pasta, but hidden ones too: soy sauce, salad dressings, soups, processed meats, even some supplements. After 30 days, reintroduce it and watch what happens. You’re likely to be more in tune with your body and tell if it’s affecting you.

The important thing is to make real-food swaps, not just trade gluten for ultra-processed “gluten-free” cookies and crackers. Those might be technically free of gluten, but they’re often loaded with sugar and starch that can cause new problems. Whole, nourishing food is the goal—vegetables, high-quality proteins, healthy fats, and gluten-free grains like rice and quinoa.

Gluten isn’t a problem for everyone, but it’s not neutral either. For many people struggling with gut issues, brain fog, autoimmune symptoms, or stubborn inflammation, removing gluten can be a game-changer. It’s not about jumping on a trend, it’s about listening to your body and being open to the idea that what we eat matters deeply.

If your body has been whispering that something’s off, gluten may be part of the story. You don’t need a label or a lab test to begin tuning in. Sometimes the most powerful step in healing is simply removing what’s getting in the way.