The Gut Issue That Might Be Confused With Gluten Intolerance

If you've ever blamed bloating, cramping, or an urgent trip to the bathroom on gluten, you're not alone. Gluten intolerance has become the go-to explanation for unexplained digestive distress. But there’s another lesser-known condition that could be behind your gut issues and it’s often mistaken for a sensitivity to gluten.

Enter fructan intolerance a sensitivity to a specific type of carbohydrate found in many of the same foods as gluten. It’s been making waves thanks to a viral TikTok by gastroenterologist Wendi LeBrett, MD, who said, “Most people aren’t actually intolerant to gluten but instead have a fructan intolerance.” So, what exactly is this condition, and how can you tell the difference?

What is fructan intolerance?

Fructans are chains of fructose molecules found in a wide variety of foods, especially wheat, onions, garlic, and certain vegetables like Brussels sprouts and broccoli. For people with fructan intolerance, these carbohydrates aren’t broken down properly in the gut often due to a lack of the enzyme alpha-galactosidase and they end up being fermented in the colon, causing gas, bloating, diarrhea, and other IBS-like symptoms.

“Fructan intolerance can look almost identical to gluten sensitivity,” explains gastroenterologist Ashkan Farhadi, MD. “The symptoms gas, bloating, cramping are very similar.”

That overlap in symptoms is what makes it so easy to mistake one for the other.

Why gluten gets blamed

Gluten a protein found in wheat, rye, and barley is a common suspect when it comes to gut distress. But what many people don’t realize is that fructans are also found in those same grains, so pinpointing the cause of symptoms without professional help or an elimination diet can be tricky.

Plus, there’s more general awareness around gluten intolerance than fructan sensitivity, so many people assume gluten is the culprit.

“People are often quick to cut out gluten, but may still experience symptoms because the real issue is with fructans,” says registered dietitian Lindsay Malone, MS, RD.

To make matters more confusing, there’s no definitive test for fructan intolerance. Instead, healthcare providers often rely on food tracking and elimination diets to identify the trigger.

5 Ways to Manage Fructan Intolerance

If your gut symptoms are persistent and don’t seem to resolve with a gluten-free diet, fructan intolerance might be to blame. Here’s how to get to the bottom of it and find relief.

1. Try a low-FODMAP diet

Fructans are one of the five types of fermentable carbohydrates included in the FODMAP group. A low-FODMAP diet, which removes foods high in these sugars, can help reduce symptoms.

Common high-fructan foods to avoid:

• Onions and garlic

• Wheat and barley

• Apples and asparagus

• Legumes and artichokes

After following a low-FODMAP diet for 4–6 weeks, work with a provider to slowly reintroduce these foods to identify which ones are causing issues.

2. Keep a food diary

Logging your meals and symptoms for a couple of weeks can help connect the dots between what you’re eating and how your gut feels. Note specific ingredients and timing, and share the diary with your doctor to guide next steps.

3. Reintroduce foods strategically

Don’t eliminate high-FODMAP foods forever many are nutritious and rich in fiber. Once your symptoms calm, reintroduce them one at a time in small portions to see what you can tolerate.

“Most patients can bring back some of these foods in small amounts without major issues,” says gastroenterologist Ellen Stein, MD. “The key is balance.”

4. Cut back on ultra-processed foods

Highly processed foods may contain hidden FODMAPs (like inulin or high-fructose corn syrup) as well as additives and preservatives that can contribute to bloating. Focus on whole, minimally processed ingredients to keep your gut calm.

5. Consider a probiotic or digestive enzyme

Over-the-counter enzymes like Beano, which contains alpha-galactosidase, may help you better digest high-fructan foods. Probiotics can also support a more balanced gut microbiome, which might improve tolerance over time.

When to see a healthcare provider

There’s no single test for fructan intolerance, but a hydrogen breath test may offer some insight. And while mild symptoms may be manageable with diet tweaks, persistent gas, bloating, or changes in bowel habits deserve a closer look.

“These symptoms are common, but they’re not normal,” says Malone. “Don’t ignore your gut. It’s trying to tell you something.”

Working with a GI specialist or registered dietitian trained in digestive disorders can help you uncover the root cause and develop a sustainable plan whether your issue is gluten, fructans, or something else entirely.

Bottom line: If you’ve cut out gluten and still feel off, fructans could be the real problem. With a little detective work and some expert guidance, you can start feeling like yourself again one bite at a time.

Enjoyed this article? Share it or subscribe to our newsletter for more health and wellness insights.