Gluten-free, But Still Gassy and Bloated? The Top 7 Causes

By Christine Doherty, ND

Gas and bloating are two of the most common reasons people come to see me. I have been in clinical practice for almost two decades and my patient population has changed a lot in that time. A decade ago I was diagnosing people with celiac and gluten intolerance and introducing them to the gluten free diet. Now with the explosion of popular press about celiac and the gluten free diet, most of the patients I see are already gluten free. This means that now I am working to identify other conditions that are co-existing with their gluten intolerance and that won’t respond to the gluten free diet alone.

I am going to walk you briefly though the most common causes of residual bloating that has not responded to the gluten free diet. The first culprit being that you’re inadvertently consuming trace amounts of gluten hiding around your house. The next top offender for causing gas and bloating in the gluten free population are other food allergies, fructose intolerance, lactose intolerance, small intestinal bacterial overgrowth, gastroparesis, pancreatic insufficiency and parasitic, bacterial and/or fungal infections. Many people with these symptoms get diagnosed with Irritable Bowel Syndrome (IBS), which is only a description of symptoms, not a cause. Let’s look at each one individually:

  1. Secretly “glutening” yourself: The first thing I always consider is trace gluten contamination. Often people aren’t as gluten free as they think they are or as they need to be. Doing a thorough inventory of some of the tricky, but common sources of gluten contamination is key. Some of the most frequent offenders are silverware drawers full of gluten crumbs, sponges that are spreading gluten around, pasta colanders, wooden utensils and cutting boards that have been used for gluten, shared toasters, foods that are that are shared by gluten eaters in the household (such as condiments, dairy or nut butters), pet food containing gluten, cosmetics, etc.

  2. Food allergies and intolerances: The most common offending foods are dairy, eggs and soy. Rarely do I see bloating as the only symptom when food allergies are the culprit, there are usually lot of other systemic symptoms like headaches, rashes, joint pain, insomnia, etc. In terms of testing, there are true food allergies which are IgE  antibody based, these are the ones tested for by the allergists but there are IgG  antibody based reactions, which are more cumulative in terms of their reactions, although they can be fast onset. The IgG will not trigger allergic shock however, only IgE will do that.

  3. Fructose and Lactose Intolerance: these are enzyme deficiencies that prevent the digestion of dietary sugars. The treatment for both ideally involves avoiding the offending sugar — either lactose found in dairy products or fructose found in specific fruits and vegetables (check out my video on YouTube on fructose intolerance). For lactose intolerance, supplemental lactase enzyme can be taken to help digest lactose better. For Fructose, there is no such enzyme, you just have to avoid the high fructose foods. Both of these are diagnosed with breath tests.

  4. Small Intestinal Bacterial Overgrowth (SIBO): We hear about good bacteria in the gut, but it should be in the colon. If it gets into the small intestine it is considered and infection and you can have significant gas and bloating. This can be diagnosed by biopsy or by breath test. Some people will respond to probiotics if they have a mild case but severe cases need to be treated with a special antibiotic called Rifaximin.

  5. Gastroparesis: when we eat the stomach usually empties within half an hour, but sometimes the stomach kind freezes, and it can take hours to empty.  This causes a feeling of uncomfortable fullness in the stomach that  is often described as bloating. It is diagnosed with a radioactive egg test for gastric emptying. I treat it with digestive enzyme successfully, but there are medications that are also used. It is often triggered by high fat foods and stress.

  6. Pancreatic insufficiency: the pancreas is known for its role in insulin production but it also plays a vital role in digestion. It secretes enzymes that help digest fat and carbohydrates. There is a stool test for elastase and fecal fat levels that can help diagnose this. The treatment is decreasing fat intake and taking digestive enzyme to help digest the fat you are still eating.

  7. Infections: I diagnose a lot of bacterial, fungal and parasitic infections in my practice using stool tests. Treatment involves restoring proper balance of good bacteria and eliminating the infection.


All of the above conditions are manageable and can significantly improve your digestion and quality of life once they are properly identified and treated. Always keep in mind you can have more than one of these simultaneously.  And don’t forget, the gluten free diet is by nature low in nutrients so often people don’t feel fully recovered even after their digestive problems have been identified and treated until their nutritional status is restored which takes on average three months with the right supplementation. Most of the conditions above can cause nutrient malabsorption, so it is key to take a high quality nutritional supplements like gluten free multi-vitamin to reverse your nutritional deficiencies.