IBS vs. Gluten Intolerance Guide: How to Tell the Difference & More

Irritable bowel syndrome (IBS) and gluten intolerance are two common gut conditions, but while they have many of the same symptoms, they have different underlying causes and require different approaches to diagnose and manage.

Because they involve similar symptoms and can be triggered by similar foods, many people mistake one condition for the other. However, it's important to understand the differences between the two conditions before making major dietary changes, as misidentifying which condition you're dealing with could lead to unnecessary food restrictions.

This article will cover:

• The key differences between IBS and gluten intolerance

• Common symptoms of each condition

• How each condition is diagnosed

• Whether gluten can cause IBS symptoms

• When a low FODMAP diet may be appropriate

• When digestive enzymes could be beneficial

Before making any major changes to your diet, it's important to speak with your healthcare provider to ensure you have an accurate diagnosis, as the digestive symptoms commonly experienced with IBS and gluten intolerance can also be signs of conditions such as inflammatory bowel disease (IBD) and celiac disease.

IBS vs. Gluten Intolerance: Quick Comparison

While similar, IBS and gluten intolerance differ in their triggers, diagnosis, and treatment. Both involve digestive symptoms and are not contagious, but gluten intolerance can also cause symptoms outside the digestive system, such as fatigue, headaches, and brain fog.

Because IBS and gluten intolerance are managed differently, it's critical to receive an accurate diagnosis before eliminating potential trigger foods. Not having a proper diagnosis can result in unnecessary restriction, which can be detrimental to both physical and mental health.

What Is IBS? 

IBS is a chronic gastrointestinal disorder classified as a disorder of gut-brain interaction (previously known as a functional gastrointestinal disorder). This means that IBS symptoms are caused by a miscommunication between the gut and brain, which influences gut motility (the movement of food and waste through the digestive tract) and gut sensitivity (making the gut more sensitive to normal digestive sensations). IBS may develop on its own or after a gut infection, known as post-infectious IBS.

IBS does not damage the intestines, but the symptoms are real and often very disruptive to daily life. There are four IBS subtypes, based on specific symptoms related to bowel movements:

• IBS with diarrhea (IBS-D)

• IBS with constipation (IBS-C)

• IBS with mixed bowel habit (IBS-M; when a person experiences constipation and diarrhea)

• IBS with unclassified bowel habit (IBS-U)

Regardless of the IBS subtype, IBS includes recurrent abdominal pain or discomfort at least 3 days per month over the past 3 months. We'll explain in more detail how IBS is diagnosed later in this article.

IBS Symptoms

IBS symptoms can vary based on subtype, but typically include:

• Abdominal pain or discomfort

• Bloating

• Gas

• Altered bowel frequency and consistency (diarrhea-dominant, constipation-dominant, or a mix of both)

• Incomplete bowel movements

• Bowel urgency

These symptoms can be unpredictable and challenging to manage and may lead IBS patients to miss work and social events. 

What is Gluten Intolerance? 

Gluten intolerance is also known as non-celiac gluten sensitivity (NCGS). While symptoms occur after eating gluten, it does not involve autoimmune intestinal damage like celiac disease.

Unlike celiac disease, there is no single diagnostic test for NCGS. Instead, diagnosis is usually made after ruling out celiac disease and wheat allergy.

Curious about the differences between the three conditions? Here's a quick summary of each:

• Gluten intolerance: Occurs when a person develops symptoms after gluten ingestion but does not experience any structural damage as a result.

• Celiac disease: An autoimmune disease affecting around 1% of the population in which the immune system mistakenly attacks the cells of the small intestine after gluten consumption. Symptoms include gas, bloating, chronic diarrhea or constipation, fatigue, weight loss, and abdominal pain. Risk factors for celiac disease include having a family member with celiac disease or having another autoimmune disorder like type 1 diabetes. It's thought that around 5% of IBS diagnoses could actually be celiac disease.

• Wheat allergy: An allergic disease where the immune system reacts to proteins found in wheat (including albumin, globulin, gliadin, or gluten). While it can involve digestive symptoms, it often also includes other symptoms such as hives, itching, or irritation of the nose and mouth, and even anaphylaxis. Like other food allergies, the only treatment is removing wheat from the diet.

Gluten Intolerance Symptoms

Symptoms of gluten intolerance can vary widely from person to person and may include both digestive and non-digestive symptoms. It includes many IBS-like symptoms, but can also include symptoms that occur outside of the gastrointestinal tract.

Common digestive symptoms include:

• Gas

• Bloating

• Abdominal discomfort

• Stomach pain

• Diarrhea

• Constipation

• Nausea

Non-digestive symptoms include:

• Fatigue

• Headaches

• Brain fog

• Joint pain

• Skin issues (such as flushing or rashes)

Symptoms typically develop after eating gluten-containing foods, and removing gluten from the diet can often alleviate symptoms.

Celiac Disease Symptoms vs. Gluten Intolerance Symptoms

Celiac disease is an autoimmune disorder, not an intolerance. One key difference between celiac disease and gluten intolerance is that in celiac disease, the immune system attacks the cells of the small intestine after gluten consumption, which damages the delicate, fingerlike projections called microvilli.

Damage to the microvilli is responsible for many of the common symptoms of celiac disease, including nutrient deficiencies, weight loss, and anemia. People with celiac disease may also develop dermatitis herpetiformis, a condition characterized by blistered, extremely itchy skin.

In contrast, there is no intestinal damage with gluten intolerance, and symptoms resolve without permanent injury.

If you suspect you may have celiac disease, it's important to get tested before starting a gluten-free diet. This is because a person with celiac disease who is following a gluten-free diet will not produce the antibodies (immune cells) detected in a celiac disease blood test. 

Gluten intolerance is slightly different from non-celiac wheat sensitivity (NCWS), which may be caused by several different components of wheat, including gluten (a protein), fructans (fermentable carbohydrates), and amylase/trypsin inhibitors (non-gluten proteins). It is also different from wheat allergy, which is an allergic reaction to wheat proteins.

People with gluten intolerance may also need to avoid rye, barley, and triticale—three other grains that contain gluten.

IBS Symptoms vs. Gluten Intolerance Symptoms

Since some symptoms and trigger foods overlap, people with IBS may mistake it for gluten intolerance and vice versa.

How Are IBS and Gluten Intolerance Diagnosed? 

While the symptoms and trigger foods for IBS and gluten intolerance are similar, they are diagnosed very differently. Below, we'll share what you need to know about how each condition is diagnosed.

IBS Diagnosis

Because IBS is classified as a DGBI, it is diagnosed according to the Rome Foundation guidelines. The most current set of guidelines, which was published in 2026, is the Rome V criteria. 

According to the Rome V criteria, IBS is defined as recurrent, but not consistent, abdominal pain or discomfort at least 3 days per month, with two or more of the following:

• Related to defecation (bowel movements)

• A change in stool frequency (how often you have a bowel movement)

• A change in stool form (the texture of your stool).

In addition, in people who menstruate, abdominal pain or discomfort should not only be related to menses.

Since IBS lacks clear, consistent biomarkers, diagnosis relies on symptom-based criteria and the exclusion of other gut conditions through stool tests, blood work, or, when appropriate, endoscopy or colonoscopy.

Gluten Intolerance Diagnosis 

Unlike IBS, which has a specific set of symptoms-based criteria used for diagnosis, gluten intolerance is a diagnosis of exclusion. Typically, that means testing for celiac disease using blood tests or a biopsy (where a small sample of tissue from the small intestine is examined) and testing for wheat allergy, if appropriate.

If those tests are negative, the next step is typically an elimination diet, removing gluten and monitoring symptoms. There is no clinically validated biomarker for gluten intolerance, so an elimination diet is currently the best method we have for identifying it.

Managing IBS and Gluten Intolerance 

Once you've determined whether you have IBS or gluten intolerance, it's important to know about the different management options. 

If You Have IBS

The most important part of managing IBS is identifying your own unique IBS triggers. Some people experience symptoms after eating high FODMAP foods, while others may experience flare-ups during stressful times. Depending on the triggers, management options for IBS may include:

• Temporary dietary reduction of FODMAPs

• Adjustments to the type and amount of fiber consumed

• FODMAP-specific digestive enzymes

• Stress management techniques such as deep breathing or journaling

• Gut-directed hypnotherapy

• Cognitive behavioral therapy (CBT)

• Medications where appropriate

In many cases, a combination of the above management strategies is needed. IBS is multifactorial, meaning that many different things can trigger it. As such, it requires a plan addressing each potential trigger you've identified.

If You Have Gluten Intolerance 

If you have gluten intolerance, the main treatment is to avoid gluten. This means reading labels and ingredient lists for gluten, preventing cross-contamination when necessary, and ensuring you eat a wide variety of different foods to promote nutritional balance.

When reading food labels, the following ingredients mean the food may contain gluten:

• Wheat (including durum, semolina, spelt, farro, bulgur, kamut, einkorn, couscous, and emmer)

• Rye

• Barley

• Triticale

• Flours (including white flour, whole-wheat flour, graham flour, self-rising flour, bread flour, cake flour)

• Wheat starch

• Wheat bran

• Wheat germ

• Wheat berries

• Seitan (vital wheat gluten)

• Malt extract

• Malt syrup

• Malted milk

• Brewer's yeast

• Soy sauce (some varieties)

While this is not a complete list, it includes some of the most common gluten-containing ingredients to look out for if you need to avoid gluten. Keep in mind that gluten-free and low FODMAP foods may overlap, but not all gluten-free foods are low FODMAP, and vice versa.

The Role of the Low FODMAP Diet 

The low FODMAP diet is frequently used to identify and manage food-related IBS triggers. FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols.

FODMAPs are food components called short-chain carbohydrates. They are poorly absorbed in the small intestine and instead enter the large intestine intact. Because FODMAPs act as prebiotics (food for your good gut bacteria), they get fermented. Fermentation produces gas, which puts pressure on the intestinal walls and can be very painful for people with extra-sensitive digestive systems (such as those with IBS).

One particular type of FODMAP, called fructan (an oligosaccharide), is a major IBS trigger for many people. In fact, research findings suggest that over 50% of people with IBS experience symptoms after consuming fructans, and other research suggests that about 70–80% of IBS patients experience symptom relief on a low FODMAP diet.

So, why the connection between IBS and gluten intolerance? Wheat, a source of gluten, is also one of the largest dietary sources of fructans. When people cut out wheat because of gluten, they're also significantly reducing their intake of fructans. In many cases, it may be the reduction in fructans, not gluten, that is responsible for the improvement in symptoms.

One way to distinguish between gluten-related disorders (such as gluten intolerance) and fructan intolerance is a short-term low FODMAP elimination diet. Because many foods contain fructans (including onions and garlic), this diet can help you determine whether fructans as a whole are a trigger or if it's truly gluten that's triggering your symptoms.

For example, if you experience gastrointestinal symptoms after eating wheat, onions, or garlic, it's likely you're intolerant to fructans. On the other hand, if you can tolerate onions and garlic just fine but develop symptoms when eating wheat, gluten (or another component of wheat) may be the culprit.

How FODZYME Can Support a More Flexible Diet 

If you've discovered your symptoms are triggered by fructans, not gluten, you may be wondering if you need to avoid wheat, onions, garlic, and other fructan-containing foods forever. Fortunately, targeted digestive enzymes can help break down fructans before they reach the large intestine, reducing fermentation and gas production.

FODZYME breaks down FODMAPs — fructan, GOS, and lactose — into more digestible carbohydrates. It's designed for people with sensitivity to high FODMAP foods and unlocks a more liberal diet through relief of occasional gas and bloating.

However, keep in mind that digestive enzymes cannot help celiac disease patients tolerate gluten. A person with celiac disease must follow a lifelong gluten-free diet to prevent damage to their intestines and to manage symptoms. However, digestive enzymes can help patients with celiac disease tolerate other fructan-containing foods, like garlic, onion, and chickpeas.

If you're unsure what's causing your symptoms, working with a registered dietitian or other healthcare professional experienced with food intolerances and digestive disorders can be extremely helpful. They can help ensure you're not avoiding too many foods, identifying your personal triggers and that you're meeting your nutrient requirements while managing your symptoms.

Try FODZYME today.

Gluten Intolerance vs. IBS FAQ

Is IBS the same as gluten intolerance? 

No, IBS is not the same as gluten intolerance. While some symptoms overlap, they have different causes, diagnoses, and treatments. IBS is a disorder of gut-brain interaction (DGBI) thought to be caused by miscommunication between the gut and the brain, resulting in changes in gut motility and visceral hypersensitivity (overly sensitive digestive organs). It is diagnosed using the Rome V criteria, and treatment may include a low FODMAP diet, stress management, gut-directed hypnotherapy, cognitive behavioral therapy (CBT), and, in some cases, medication.

In contrast, gluten intolerance is an intolerance specifically to gluten, a protein found in wheat, rye, barley, and triticale. We currently don't have a test to diagnose it, so it is typically a diagnosis of exclusion based on symptoms. This means it is diagnosed only after other testable conditions have been ruled out. The main treatment is avoiding gluten in the diet.

Can gluten cause IBS symptoms? 

No, gluten itself is not considered a cause of IBS symptoms. However, many gluten-containing foods may trigger symptoms because they're high in FODMAPs. For example, the fructans found in wheat may be responsible for triggering symptoms in many people with IBS. That said, some individuals do have a true gluten sensitivity, while others may be reacting to the FODMAPs. This highlights the importance of proper diagnosis, so you can use the appropriate treatment.

Can you have IBS and gluten intolerance at the same time? 

Having a diagnosis of IBS does not rule out the possibility of also being gluten intolerant, and the two conditions can overlap. Some people with IBS benefit from reducing gluten-containing foods, but often, this is due to unintentionally also reducing fructans in their diet. It's extremely difficult to untangle the two conditions, which is why it's important to work with a knowledgeable healthcare professional.

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