Why Does Gluten Make My Stomach Hurt? A Simple Explanation

“Why does Gluten feel like trouble?”

BY STEPHNIE @the Brimly Test Kitchen

January 23, 2025

Image Source/Editors @ Brimly

10 minute Read

INFO CONTENT

FEATURE ARTICLE

Objective VIEW

“Gluten is not inherently bad, but for those with certain conditions, it can act like a trigger, setting off a cascade of health issues that go far beyond the gut."
– Dr. Alessio Fasano

For some people, eating a slice of bread or a bowl of pasta brings pure joy. But for others, those same foods can lead to a whole lot of discomfort. Bloating, cramps, or even worse symptoms can follow. If you’ve ever experienced discomfort after eating gluten, it might feel frustrating or even confusing. Many individuals find the effects of gluten to be deeply personal, as though their digestive system is uniquely affected. This article breaks down, in simple terms, how gluten interacts with your digestive system and why it can lead to pain for certain individuals. By the end, you’ll have a clearer understanding of what gluten does in your body and what you can do to feel better.

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What Is Gluten, Anyway?

Gluten is a protein found in wheat, barley, and rye. It’s what gives bread its chewy texture. It also helps dough maintain its shape. It acts as a critical structural component, offering elasticity and strength to baked goods, allowing them to maintain their form and texture. In the absence of gluten, bread would lose its structure and crumble, cakes would fail to rise and maintain their form, and pasta would disintegrate during the cooking process. While most people can digest gluten without any complications, some struggle. Their bodies can’t fully process gluten. This sets off a chain reaction that leads to unpleasant symptoms. For these individuals, even small amounts of gluten can be problematic. To understand this better, it’s important to know how the digestive system handles gluten and why things can go wrong.

How the Digestive System Normally Processes Gluten

When you eat a piece of bread, your digestive system goes to work. Enzymes in your stomach and small intestine break down the food. Carbohydrates, fats, and proteins are separated into smaller components. For proteins like gluten, this involves breaking them into amino acids and peptides (these are the building blocks of protein). Normally, this process works smoothly. The gluten is broken down and absorbed into the bloodstream, fueling the body. However, some bodies don’t break down gluten efficiently. This can result in significant digestive discomfort. The underlying causes of this issue are diverse and depend on individual conditions. It often ties back to conditions like celiac disease, non-celiac gluten sensitivity, or a wheat allergy. Each of these conditions disrupts the digestive process in its own unique way, making gluten a source of discomfort rather than nourishment.

Video courtesy of TED-Ed

This TED-Ed video explores the science behind gluten, from celiac disease to gluten sensitivity, with insights from William D. Chey. A concise and informative look at why gluten has become a modern dietary concern.

Celiac Disease

Celiac disease is an autoimmune disorder. It affects about 1% of the population. In people with celiac disease, gluten doesn’t pass through the digestive system quietly. Instead, it sets off an immune response. When gluten reaches the small intestine, the immune system misfires. It identifies gluten as harmful. This triggers an attack that damages the lining of the small intestine. The immune system targets the small structures known as villi, which play a crucial role in nutrient absorption. Villi absorb nutrients from food. When damaged, this leads to more than just stomach pain. People with celiac disease may experience bloating, diarrhea, or constipation. Other symptoms include weight loss and nutrient deficiencies, like anemia. The damage can also cause fatigue and long-term health complications. The only effective treatment is to completely avoid gluten. Even small amounts can trigger symptoms and cause lasting harm. It’s not just a matter of choice; for those with celiac disease, gluten-free living is essential to avoid serious health risks.

Non-Celiac Gluten Sensitivity

Not everyone who reacts to gluten has celiac disease. Non-celiac gluten sensitivity (NCGS) is another condition. It causes symptoms without the autoimmune damage seen in celiac disease. The exact mechanisms behind NCGS aren’t fully understood. However, gluten is known to irritate the lining of the digestive tract in some people. This irritation can cause inflammation. Symptoms often include stomach pain, bloating, fatigue, and brain fog. Bowel irregularity is also common. Unlike celiac disease, NCGS doesn’t damage the gut over time. However, it can significantly impact quality of life. Many people find that avoiding gluten improves their symptoms, even if their condition is less clearly defined. Living with NCGS often means navigating a confusing landscape. Gluten-free options can bring relief, but the lack of a definitive diagnosis can leave people questioning their choices. Still, for those affected, reducing or eliminating gluten can be life-changing.

Wheat Allergy

A wheat allergy is different from celiac disease or NCGS. It involves a traditional allergic reaction to proteins in wheat. Gluten is only one of these proteins. When someone with a wheat allergy eats wheat, their immune system overreacts. This triggers the release of chemicals like histamines. Symptoms can include nausea, stomach cramps, and vomiting. But the reaction isn’t limited to the digestive system. It may also cause skin rashes, swelling, or even anaphylaxis in severe cases. Unlike celiac disease and NCGS, a wheat allergy can affect multiple systems in the body. Immediate medical attention is sometimes required. Avoiding wheat entirely is the best way to manage this condition. For people with wheat allergies, vigilance is key. Reading labels, asking about ingredients, and carrying emergency medication can be a necessary part of daily life. While it’s challenging, managing a wheat allergy helps prevent potentially life-threatening reactions.

Why Some People Without a Diagnosis Still Feel Symptoms

Even if you don’t have celiac disease, NCGS, or a wheat allergy, gluten might still bother you. This is often due to other factors. For instance, gluten-containing foods like bread and pasta are high in FODMAPs. These are fermentable carbohydrates that can cause bloating and discomfort. People with irritable bowel syndrome (IBS) are especially prone to this. Another possibility is gut dysbiosis. This is an imbalance in gut bacteria that makes it harder to process certain foods, including gluten. Stress and overeating can also exacerbate digestive issues. Sometimes, it’s not just the gluten but the context in which it’s consumed. A combination of factors may create the perfect storm of discomfort. By addressing overall gut health and eating habits, some people find relief even if gluten isn’t the primary culprit. Understanding the broader picture can help identify solutions that go beyond simply avoiding gluten.

What to Do if Gluten Makes Your Stomach Hurt

If gluten seems to be causing your stomach pain, take action. Start by consulting a doctor or dietitian. They can determine whether you have celiac disease, NCGS, or another condition. Don’t self-diagnose. Accurate testing often requires that you keep eating gluten before evaluations. Keeping a food diary can also help. Write down what you eat and any symptoms you experience. This can reveal patterns and trigger foods. An elimination diet might also be useful. Temporarily remove gluten and then reintroduce it to confirm if it’s the culprit. Always do this under professional guidance to ensure proper nutrition.

Supporting gut health is equally important. Eat fiber-rich fruits and vegetables. Include fermented foods like yogurt and kimchi in your diet. Staying hydrated also helps maintain a healthy gut. If you decide to avoid gluten, choose nutrient-dense alternatives. Avoid processed gluten-free products that are often low in fiber and high in sugar. For those who continue eating gluten, mindfulness during meals can make a big difference. Eating slowly and managing stress can reduce symptoms. Taking proactive steps helps alleviate immediate discomfort and builds a strong foundation for long-term digestive health.

If you decide to avoid gluten, opt for nutrient-dense alternatives such as quinoa, brown rice, and sweet potatoes. These foods offer essential carbohydrates along with vitamins and minerals that support overall health. Be cautious with processed gluten-free products. They tend to be low in fiber and often contain added sugars, which can negate the benefits of going gluten-free.

Building a healthy gut requires consistency and intentional effort. Adding prebiotic-rich foods such as bananas, garlic, and asparagus helps feed the beneficial bacteria in your gut. This creates a more balanced microbiome. Establishing a regular meal schedule is equally important. It helps stabilize digestion, prevents overeating, and keeps your system functioning smoothly. A well-regulated gut provides immediate relief and promotes long-term health. By adopting these strategies, you lay the foundation for a thriving digestive system and improved overall wellness.

The Bottom Line:

Gluten isn’t a problem for most people. But for those whose digestive systems don’t agree, it can cause significant discomfort. Understanding how gluten interacts with your gut is the first step toward relief. It could be celiac disease, NCGS, or another related issue—but paying attention to your body's signals is crucial. Seeking professional guidance ensures you make informed and effective choices. While some individuals find that adopting a gluten-free diet greatly improves their well-being, others do not find it necessary or beneficial. Many people continue to enjoy bread and pasta without experiencing any adverse effects. The key is figuring out what works best for you. Your gut deserves care and attention. After all, a happy gut leads to a happier you. Taking the time to explore your relationship with gluten can open the door to better health and a better quality of life.