When You Have Celiac But Gluten Isn’t Causing Your Gastrointestinal Issues

What happens when an individual with diagnosed celiac experiences gastrointestinal (GI) symptoms? GI issues such as bloating, constipation and diarrhea are common celiac symptoms, so an individual may assume such discomfort is the result of inadvertently consumed gluten or cross-contamination. While this certainly could—and for some individuals, will—be the case, gluten may not be the cause of these symptoms for others.

“Though the majority of patients with celiac disease have a marked improvement or resolution of symptoms after starting a gluten-free diet, about a quarter to a fifth of patients at any given time report that they have either persistent symptoms (i.e., the symptoms did not entirely go away) or recurrent symptoms (i.e., the symptoms initially improved and then came back),” explains Benjamin Lebwohl, MD, MS, director of clinical research at the Celiac Disease Center at Columbia University. “This is one of the most common reasons people seek evaluation at a celiac disease center. The most common cause of these symptoms is gluten exposure, but there are a number of other causes.”

Something feels “off”

Not every GI symptom is cause for concern. Individuals with diagnosed celiac can experience GI episodes like anyone else. “It is common for patients with celiac disease to assume that an episode of gastrointestinal distress is due to gluten exposure, but they are prone to the same kinds of episodes of food poisoning or gastroenteritis as everyone else,” says Lebwohl.

One’s dietary choices, for example, can lead to GI upset. As Laura Manning, MPH, RD, CDN, clinical nutrition coordinator at The Mount Sinai Hospital, points outs, certain items in larger quantities—such as alcohol, sugar or even too much coconut oil—can cause diarrhea in some individuals. Manning also notes that choices within the gluten-free diet can lead to constipation.


“Very often, someone will embrace the gluten-free diet/lifestyle and then purchase a lot of foods that are packaged—gluten-free cookies and breads and so forth”—and these products contain refined flour as opposed to whole-grain ingredients, Manning says. While these items taste good, splurging on them “can also lead to constipation.”

For these patients, Manning will review their dietary habits and suggest healthier alternatives. “I probably can identify that they have a lot more processed gluten-free products in their diet and will have them switch over to whole grains in their most wholesome form, as opposed to milling down the flours,” she says. She recommends that patients focus on including whole grains such as quinoa and brown rice, fruits and vegetables, and also increase their hydration.

Accidental gluten ingestion might not explain recurring GI distress in someone with celiac. “When these [symptoms] occur frequently, gluten exposure is a possibility, but it is important to consider other causes beyond celiac disease,” says Lebwohl. “This should be done with the guidance of a clinician experienced in the management of celiac disease.”


Is gluten the culprit?

The first step in determining whether frequent GI symptoms are caused by gluten exposure is visiting a physician.

First and foremost, explains Rupa Mukherjee, MD, attending gastroenterologist at Beth Israel Deaconess Medical Center in Boston, it is “important to make sure that the diagnosis [of celiac] has been confirmed, since there are other causes for villus atrophy, or inflammation of the small bowel, that can overlap with celiac.”

Following a confirmed celiac diagnosis, “The first step would be making sure through a meticulous dietary evaluation that there isn’t gluten exposure from some source that the patient is not aware of,” she says. To obtain this dietary history, Mukherjee says that “it’s often helpful to do this under the guidance of a celiac dietitian—someone trained and experienced in celiac-related dietary issues.”

“I generally ask every patient of mine with celiac disease what their gluten reaction is—if they even have one, since not everyone does,” says Mukherjee. “Some patients can be asymptomatic, and for them, that’s very frustrating because they don’t know if and when they have been exposed to gluten.”


Those patients who do experience symptoms “have a good sense of what their gluten reaction is, so they can tell soon after eating out if they were exposed to gluten or not.” She also points out that “the symptoms that characterize a patient’s gluten reaction can change with time.”

A patient should share every symptom with his or her physician, and disclosing new symptoms is especially crucial. “But it’s important to put it into perspective that if a patient develops a new symptom, such as constipation, that this is not necessarily due to having celiac disease or getting exposed to gluten,” Mukherjee says. “In these cases, it’s important that the patient discusses new symptom onset with their physician or gastroenterologist.”

Once it has been determined that a patient with confirmed celiac is not being exposed to gluten yet is still experiencing GI distress, Mukherjee says, “there are other etiologies/conditions for ongoing symptoms that need to be considered and evaluated for.”


Two possible causes

A patient with diagnosed celiac who is strictly adhering to the diet but experiencing diarrhea and abdominal cramps could have microscopic colitis. The condition, Lebwohl explains, occurs when “the colon (large intestine) becomes inflamed on a microscopic level—the naked-eye appearance of the colon is normal (or sometimes slightly red) on colonoscopy, but biopsies show injury.”

The cause of this condition varies, “but in some patients medications such as anti-inflammatory medicines such as ibuprofen can be a trigger,” says Lebwohl. However, gluten could still play a role. “In people with celiac disease, gluten exposure can sometimes be a trigger [of microscopic colitis].

“There are several medications that are used to treat microscopic colitis, including bismuth (i.e., Pepto-Bismol), and, in some cases, medications that decrease inflammation in the intestine such as budesonide,” says Lebwohl. For individuals with microscopic colitis caused by taking anti-inflammatory medicines, “simply stopping the medication is often sufficient to result in improvement.”


Another possible condition, small intentional bacterial overgrowth (SIBO), occurs when there are excessive bacteria in the small intestine.

“Small intestinal bacterial overgrowth occurs when the quantity of bacteria that live in the small intestine increases,” Lebwohl explains. “In the normal state of affairs, bacteria are most abundant at the end of the small intestine (the ileum), but in SIBO, bacterial quantities increase closer to the middle of the small intestine (jejunum).” As a result, a person can experience “difficulty digesting fats and impaired absorption of certain nutrients, such as vitamin B12.”

Diagnosis and treatment of SIBO are relatively straightforward. According to Lebwohl, “this condition is most commonly diagnosed via a breath test that measures bacterial quantities after ingesting a sugar compound (glucose or lactulose), and can be treated with a course of antibiotics.”

Irritable bowel syndrome

Individuals with diagnosed celiac could also have irritable bowel syndrome (IBS). IBS is a functional bowel disorder, a condition “defined by the presence of typical symptoms [that] span everywhere from the mouth all the way to the anus,” explains William D. Chey, MD, FACG, AGAF, FACP, RFF, medical director of the Michigan Medicine Bowel Control Program.


“[Functional bowel disorders] are multifactorial in terms of their cause,” Chey says, meaning that determining the specific reason such conditions occur is often not possible. “It would be wonderful to be able to say to you, well, they’re all related to abnormalities in the ways the bowels contract and in motility, or they’re all related to problems with brain/gut interactions and a visceral sensation in the GI tract to any of a variety of different kind of stimuli to any kind of food or stress. But the reality is they’re more complex than that. So while those types of factors are important, a host of other factors likely also play a role.”

Functional bowel disorders are quite common. “Probably on the order of 30 to 40 percent of people in the general population have GI symptoms at some point in time over the course of the year,” says Chey. “Probably 20 to 30 percent will qualify for a formal diagnosis of one of those functional GI disorders.”

IBS is “defined by the presence of abdominal pain and altered bowel habits, and that can be either diarrhea, constipation or a combination of both,” Chey explains.


IBS is a tricky condition to diagnose. “I think what distinguishes IBS is the frequency and severity and burden of illness associated with a person’s GI symptoms,” Chey says. “IBS is defined by the presence of abdominal pain and altered bowel habits, and when patients are having those symptoms frequently, let’s say on a weekly basis, and they’re severe enough to be affecting a person’s quality of life, to me, that constitutes an illness burden that is consistent with the diagnosis of IBS.”

A hallmark of IBS is that illness burden. “Somebody that’s having fairly frequent symptoms [that are] affecting their ability to be able to carry out their activities, those patients…should get evaluated to make sure they have IBS,” Chey says, and not the “number of things that can mimic IBS but that are treated very, very differently than IBS.”

It is important to note that celiac can be misdiagnosed as IBS. “There is clearly a small subset of patients who are mistakenly diagnosed with conditions like IBS but are subsequently found to have celiac disease, and when they go on a gluten-free diet, they get complete resolution of their symptoms,” explains Chey.


As Lebwohl notes, “Irritable bowel syndrome is present in 10 to 15 percent of the population, far more common than celiac disease (which is present in a bit under 1 percent of the population), and so it’s quite common for people with celiac disease to also have irritable bowel syndrome.”

Mukherjee points to a study at the Beth Israel Deaconess Medical Center, which found “in our cohort of patients with celiac disease, that nearly 10 percent of patients had irritable bowel syndrome as a concurrent condition that was likely propagating their celiac symptoms.”

IBS can occur at any point in individuals with celiac. “It can predate the diagnosis of celiac disease or occur at a later time after the diagnosis of celiac disease,” explains Mukherjee. “Certainly a patient who has celiac disease for years and is symptom free on a gluten-free diet with normal lab results can develop a motility disorder as a separate condition….”

Currently, there is no one-size-fits-all treatment for IBS. Some individuals experience tremendous benefits on the FODMAP diet (see sidebar). FODMAPs are a group of “fermentable carbohydrates naturally occurring in foods that are essentially healthy for us, but for some reason certain people cannot tolerate them and they get extreme pain, gas, bloating, constipation and diarrhea when they’re eaten in such large quantities,” explains Manning.

“With FODMAPing, you can learn what your trigger foods are,” she says. “The FODMAP diet will eliminate all of those fermentable carbohydrates for a short period of time.” Manning advises that “it does have to be done with the guidance of a dietitian that has some expertise in it.” After elimination, “give yourself a chance to settle down, and then you work each fermentable group back in strategically to be able to figure out what those trigger foods are.”

The goal through this removal and reintroduction, Chey explains, is “to determine a person’s sensitivities to individual FODMAPs and then tailor a person’s diet based upon that reintroduction information to establish their maintenance diet. And that’s what they stay on. They don’t stay on the full elimination diet.”

The diet has been quite successful. “Probably almost 60 percent of patients with IBS get relief from their bloating and pain with low FODMAP,” says Chey. “That being said…a significant proportion of patients don’t get better with low FODMAP.”


Acid reflux, commonly known as heartburn, occurs when the stomach contents reflux, or back up, into the esophagus—the tube that spans from the mouth to the stomach—and sometimes into the mouth. When this condition persists, it is also called GERD (gastroesophageal reflux disease).

“Any patient with celiac disease that is under good control on a gluten-free diet can develop another GI condition like GERD with time that is not necessarily related to their celiac disease, in the same way that someone can develop a food sensitivity, such as lactose or soy, with time,” Mukherjee says. “I see this frequently in my GI clinic.”

For patients experiencing acid reflux, diet and lifestyle choices can play an important role. Manning offers heartburn patients a number of tips to reduce foods and drinks “that would irritate the stomach lining and/or cause more reflux,” including fried items, citrus fruits and large quantities of coffee and tea.

When it comes to lifestyle, she also notes the importance of avoiding eating late at night as well as eating small, frequent meals instead of three large ones. Daily routine can also affect heartburn. “I ask people what they do for a living,” she says. Specifically, she asks, “Are you sitting at a desk in a bent-over position all day? Do you eat at your desk?” These are important aspects to cover, because food cannot pass through the GI tract nearly as easily as it would for someone who goes for a quick walk after eating. Even clothing can have an impact on symptoms. Manning asks patients, “Are your pants very tight? Do you wear a tight belt? Those are also really subtle, but they can make a huge difference.”

Patients with another type of heartburn, functional heartburn, “don’t necessarily have evidence of acid reflux,” says Chey. This means that they “have symptoms that for all the world look like acid reflux, but there’s no identifiable evidence of acid reflux.” These individuals, Chey says, “respond to behavioral techniques, so deep relaxation techniques or cognitive behavioral therapy seem to work just as well as any of the medications we have.”

Food intolerance and malabsorption

Food intolerance or malabsorption can also cause GI issues. In individuals with celiac, Manning notes that “a lot of patients also have a lactose intolerance. That’s super common.” For these individuals, “…the most common symptom of lactose intolerance is diarrhea, gas, bloating.” To determine whether lactose is causing the symptoms, “I’ll have to tease that out and see whether they are having copious amounts of lactose.”

Another possible cause of GI distress is malabsorption of fructose, a type of sugar. “Patients who suffer from fructose malabsorption cannot absorb fructose completely in their small intestine,” says Mukherjee. “This can be experienced as abdominal pain, cramping, gas, bloating, abdominal distension. Diarrhea can develop due to the undigested particles of fructose. “

When this malabsorption occurs, “the undigested or leftover fructose travels to the colon, where it is fermented by colonic bacteria. The bacteria produce gas, which causes the intestines to swell.” When it comes to treating this, she says that management hinges on “limiting high-fructose foods or, in other words, a low-fructose diet. It is often helpful to start a low-fructose diet, also called the FODMAP diet, with the help of a dietitian.”

If you’re experiencing frequent GI distress in spite of following a gluten-free diet, don’t assume hidden gluten is the culprit. Visit your doctor. Together, you can determine the cause of your symptoms—and effective treatments.

Susan Cohen is a New York freelance writer. She contributes regularly to Gluten-Free Living.

Learn more about the health and medical experts who who provide you with the cutting-edge resources, tools, news, and more on Gluten-Free Living.
About Our Experts >>


Leave a Reply

Your email address will not be published. Required fields are marked *