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  • Dr. Vikki Petersen D.C, C.C.N
    Dr. Vikki Petersen D.C, C.C.N

    Gluten-Free But Still Feeling Ill

    Reviewed and edited by a celiac disease expert.

      Journal of Gluten Sensitivity Spring 2010 Issue. NOTE: This article is from a back issue of our popular subscription-only paper newsletter. Some content may be outdated.

    Caption: Some don't recover fully on a gluten-free diet alone. Photo: CC-Evil Erin

    This article originally appeared in the Spring 2010 edition of Celiac.com's Journal of Gluten-Sensitivity.

    Celiac.com 10/22/2010 - More and more we’re hearing from frustrated patients who, despite being vigilant about their gluten-free diet, continue to suffer health problems.

    I have been involved in the field of celiac and gluten sensitivity for over 15 years and am delighted by much of the recent increased awareness and attention given to the area.  But I’m also concerned about the lack of assistance given to many patients who have been definitively diagnosed with either celiac disease or gluten sensitivity.  While being correctly given the advice to not eat gluten, they are not provided with a follow-up program to address and treat the secondary effects of gluten sensitivity.  This oversight condemns many to ongoing ill health.

    The focus of this article is on the types of conditions we see clinically with our patients, some of the recent research that corroborates our findings, and steps you can take to address the underlying root cause of these problems.

    Leaky Gut

    Also known as increased intestinal permeability, a leaky gut refers to a loss of integrity of the lining of the small intestine.  Recall that the small intestine is approximately 23 feet in length and has the surface area of a tennis court.

    Gluten, in the sensitive individual, is a known cause of leaky gut, but in a perfect world the elimination of gluten would allow healing to occur resulting in an intact, healthy intestinal lining.

    Alas, we do not live in a perfect world and other factors contribute to the health of the gut.  Infections in the form of parasites, amoebas, bacteria, and the like, can certainly contribute to continued increased permeability.  Likewise, other food reactions, chief among them dairy, can cause persistent irritation and thereby prevent healing.  Imbalance of the beneficial bacteria or microbes that comprise the microbiota of the intestine, as well as nutritional and pancreatic enzyme deficiencies, are also suspected to limit healing.

    Let’s take a look at each of these individually:


    Whether one has celiac disease or is gluten sensitive, one thing is for sure, one’s immune system has been overtaxed due to the presence of gluten in the diet.  Depending on the age at diagnosis, it is often several decades of stress that the immune system has undergone.

    Such an overburdened immune system is unable to be as vigilant as a healthy one and as a result it allows such organisms as parasites, amoebas or bacteria to infiltrate the body.  Some estimates suggest that the digestive tract is normally exposed to a pathogenic organism every 10 minutes.  A healthy intestinal immune system is able to identify and eradicate those organisms as part of its normal activities.  An unhealthy immune system often “misses” such organisms and they happily take up residence in the small intestine.

    Interestingly, some of these organisms create crypt hyperplasia and villous atrophy that appears the same as that caused by gluten.  Imagine the frustration of a patient who is being told by their doctor that they are not following their diet when indeed they are.  What’s being missed?  The presence of an infectious agent.

    In the 2003 American Journal of Gastroenterology, researchers reported a large percentage of small intestinal bowel overgrowth (SIBO) in celiac patients with persistent GI symptoms despite adherence to a gluten-free diet.  These patients were off gluten, as instructed, but were still having diarrhea due inhospitable organisms in their intestines.

    This segues nicely into the next area I want to discuss – dysbiosis or imbalance of the friendly bacteria in the small intestine.


    The population of organisms found in the intestines of celiac patients (treated with a gluten-free diet or not) is different from that found in healthy control groups.  The ratio of good bacteria to bad was found to be reduced in celiac patietnts regardless of whether their celiac disease was active or inactive.  Because the “bad” bacteria are pro-inflammatory in nature, they can be responsible for creating some of the initial problems with celiac disease, as well as helping to perpetuate them despite following a gluten-free diet.

    In the August 2009 Scientific American, Dr Fasano made a very interesting statement regarding these microbes or probiotics as relates to the age of initiation of celiac disease.  He stated: “Apparently they [probiotics] can also influence which genes in their hosts are active at any given time.  Hence, a person whose immune system has managed to tolerate gluten for many years might suddenly lose tolerance if the microbiome changes in a way that causes formerly quiet susceptibility genes to become active.  If this idea is correct, celiac disease might one day be prevented or treated by ingestion of selected helpful microbes.”

    Isn’t this fascinating?  If you haven’t read the complete article I encourage you to do so, but it is sufficient to say there is scientific discussion that entertains the notion that a healthy microbiome or probiotic population is not only anti-inflammatory (a good thing to help prevent many diseases) but may actually act as a “switch” that turns on and off the expression of certain genes.

    Therefore, part of our program is to examine the population of the microbiome through laboratory testing, and supplement as needed, to support a healthy anti-inflammatory population.  In the past we typically prescribed probiotics only for a few short months following the eradication of a pathogenic organism.  But in the last several years it has become clear that our patients’ clinical profile is much more stable with continued probiotic supplementation.

    Dairy Sensitivity

    It can be difficult to confront major changes in one’s diet.  Removing gluten is definitely a big challenge and sometimes my patients look at me forlornly when I simultaneously recommend the elimination of dairy products.  I try to encourage them by promising that organic butter is allowed and by quickly recommending my favorite coconut ice cream, as well as cheese and milk substitutes.

    Contrary to the passing thought that I wish to be cruel, there is excellent documentation to back up what we’ve seen clinically for years - gluten and dairy are truly not our friends.

    The majority of the world’s people are lactose intolerant.  Populations such as Asians, African Blacks, those of Jewish descent, Mediterraneans, Mexicans and North American Blacks all exceed 70% intolerance to lactose. 

    Note that many drugs and supplements may contain lactose as well, so be vigilant.

    Estimates suggest that we retain the enzyme to digest our human mother’s milk for 2 to 5 years and after that milk from any mammal is likely toxic because it’s too high in protein and phosphorus, making proper digestion impossible.  Human milk is very low in protein but rich in essential fatty acids.

    Casein, a protein from milk, is strongly associated with allergic reactions.  Therefore putting lactose and casein together presents double jeopardy to the body.  In this country, milk contains more toxins per gram than any other food, so you can see that there’s great cause for concern.

    Earlier we spoke of leaky gut.  Dairy stops the formation of glucosamine in the intestine making it one of the primary causes of leaky gut.

    I could expand on this further but perhaps we’ll save that for a future article.

    Nutritional Deficiencies

    When we eat, the ultimate goal is that the food will be broken down into components that can be assimilated into the bloodstream and delivered as fuel to all our trillions of cells.  Discovering that one is sensitive to gluten and eliminating it goes a long way toward achieving this goal.  However, some vitamins and minerals should be tested to ensure that their levels are normalizing on a gluten-free diet.  Otherwise good health may be a fleeting target.

    Folic acid, vitamin B12, Iron and Vitamin D levels are all very important to measure.  Supplementation is often needed to optimize the levels of these substances.  Follow-up testing ensures that this objective has been achieved or maintained and should be part of a comprehensive program.

    Discovering that you’re gluten sensitive and following the diet should be rewarded with dramatically improved health.  If that is not the result, other problematic factors need to be isolated and treated.  Such a program is not difficult and is well worth the effort.

    Please let me know if I can answer any further questions.

    To your good health!

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    Dr. Petersen and her staff really knows their stuff! I have been to their practice at HealthNow Medical Center and they are all truly wonderful! After seeing multiple doctors they got to the root cause of my problem! Hurray!

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    I loved all the information given here, but was disappointed that one important aspect of all of this was left out: that gluten free is a legal term and does not mean 'zero gluten.'


    Patients are seldom informed that the foods they eat can have varying levels of gluten, and that some celiacs who are more sensitive might have to avoid certain brands or foods. My daughter consistently reacts to foods that are between 10ppm and 20ppm of gluten, so she has to be more selective in her gluten free choices, for example.


    Also, just like eating too much low calorie food can still make us fat, eating too much 'gluten free' food can still overload our systems with too much gluten, because again, they are not 'zero gluten' foods. Without that understanding of the term, it's no wonder many of us can't figure out how to eliminate enough gluten to heal and stay healthy.

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    I was one of those still having symptoms on a gluten-free/Dairy free diet. It wasn't until I quit eating carbs with meats which causes putrification and cut back from foods that make one acidic (corn, soy, potatoes, chips, COFFEE, some meats) in favor of more foods that made me more alkaline (greens, almonds, fruits, veggies) did I become symptom free.

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    Great article, not that I understood everything. Every morning about 20 minutes after waking up, I have a very loose stool. My daughter is diagnosed with gluten intolerance. Just wondering. My symptoms started about 2-3 months ago.

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    Thank you for writing this article - It was determined that I had celiac disease 10 years ago and have since tried to cut out as much dairy as possible for the reasons you listed above and it has helped. Thank you

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    This describes my daughter's experience, except she did not have parasites (she was tested for this) she was simply unable to tolerate dairy or soy. Once she eliminated these plus the gluten her stomach was able to heal.

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    The health of many celiacs also does not improve due to fugitive gluten in the environment–rather than directly from food, beverage or cosmetic products. Gluten contamination is molecular in nature and gluten transported by air reaches the intestines after being inhaled either through the nostrils or mouth. Gluten is also unwittingly carried into the mouth on fingers which have touched surfaces to which gluten has been carried by others, human or pet. Both methods occur similarly to how germs are spread. It is critical this be unquestionably documented by researchers and steps taken to remove gluten from the manufacturing for those who are gluten sensitive to ever be truly well.

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    A great education for those of us that wonder why we are still not totally healthy. A leaky gut has also given me many more allergies to all kinds of food. Recently I went on a 4 day rotation allergy diet in an effort not to become allergic to more foods and lose the allergies that I have.

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    You're on the right track but the main cause of bacterial imbalance in the gut is ANTIBIOTICS. Gluten DOESN'T cause the problem, GLUTEN SENSITIVITY happens AFTER the gut bacteria are affected & all the 'GOOD' bacteria have been killed off by ANTIBIOTICS. CHLORINE is also another cause of this, also ALL SOLVENTS.


    I have had 'coeliac disease' for most of my life, but this started after extensive use of antibiotics for a recurring 'kidney infection' when I was young (nephritis.) The 'kidney infection' happened after I was treated with experimental antibiotics for a mysterious 'tummy bug' that I developed while staying at my Grandparents. (I used to spend all day at his Petrol Station & Garage, playing around used oil etc, & hanging round the gas pumps). Also, they ate a very refined diet, compared to the 'whole foods' I was used to at home.


    After this I developed 'Chrohn's disease' & suffered diarrhea & immune disorders for 20 years until I had full blown 'Chronic fatigue'. After a few more years I was finally diagnosed 'Coeliac', but despite being on the diet for over 10 years, still have a constant struggle with my health.


    I have found that MILK is a big problem, but also ALL GRAIN STARCHES, also POTATOES & TOMATOES, even QUINOA, SOY, BUCKWHEAT etc. (Read "No More IBS" by Carol Sinclair, all the doctors have!!!).


    Also mushrooms & yeasts are a problem. I have read that Coeliac people should avoid ALL FUNGI, especially if they are Blood Type O (I am).


    I find as long as I stick to a simple high protein diet with lots of veges, I am fine. I can also enjoy coffee & chocolate, but all LOLLIES are out because they are all made with glucose syrup from wheat or corn, or contain MODIFIED STARCHES which are dietary suicide for ANYONE, but particularly for those with 'coeliac disease'.


    Also, products such as 'unsweetened' carob should be avoided, as they are sweetened with LACTOSE, which is a huge problem if you are coeliac (also watch out for Homeopathic pilules also sweetened with LACTOSE)


    Also apparently MALTODEXTRIN is very bad for coeliacs as it provokes the 'allergy', but it is being sneaked into all processed foods, along with SOY, CORN & MILK SOLIDS. According to WHO, the top 5 allergy provoking foods are WHEAT, DAIRY, SOY, CORN & PEANUTS, but various lists include EGGS, SHELLFISH, etc. Apparently allergies develop because of an inability to digest the proteins in these foods. So obviously will be a big problem for those with POOR DIGESTION or 'coeliac disease'.


    I had a noticeable allergy to BARLEY & OATS, many years before I was diagnosed coeliac (also CHEESE)


    However, after eliminating the GRAINS from my diet, I have found that I no longer have a 'problem' with eggs, shellfish & other protein foods. (cheese is still a problem) However, these MUST be combined correctly with other foods, or else will cause problems. (ie PROTEINS should NOT be consumed with starches, as each blocks the correct digestion of the other.


    My condition is also made worse by exposure to any solvents, including diesel, petrol, glues, paints, even household cleaners. All these things DESTROY our mucous membranes (not only in the gut), so have a major effect on digestion.


    The other factor that is COMPLETELY IGNORED, both by doctors & squeamish parents, is PARASITES. Children particularly, are infested with many different parasites, which if allowed to proliferate, can totally destroy their digestion as well as overall health. This is also relevant to ALL adults, especially those who have exposure to animals, soil or sick people, or pooey nappies etc.


    There is a Naturopath in Tauranga who is having great success with 'curing' many people with chronic health problems, including allergies & chronic fatigue (ME). He has a program which kills parasites, replaces lost minerals & boosts hormone production, which then allows the body to 'cure' itself.


    My 'coeliac' daughter who has been ill for 7-8 years & had a raft of 'teenage' & 'women's problems' developing, was 100% better in ONE MONTH. She is now healthy & playing sport competitively, & is also HAPPY & confident as a result of her new-found good health.


    Similarly, I took a friend from England who had been ill & tired for twenty years to see him. She had allergies, pain, tiredness etc, but was 'cured'in ONE MONTH, even though she only partially completed his program. (didn't finish the mineral replacement course)


    So I encourage you to 'think outside the square'. The medical industry really has no interest in 'curing' coeliac disease, because there is a HUGE INDUSTRY based on providing 'special foods' etc. There is NO MONEY in it for them if people treat themselves by going on a HEALTHY diet. Also there is more money for GPS & specialists in managing our (bad) health, than if we get well, so they will never let you, as I found from my own experience.


    As it is, I have not needed to go to a doctor for many years now, other than to get forms signed for WINZ, as I have been getting DISABILITY allowance for special foods & alternative treatments for some years now.


    cheers Dave

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  • About Me

    Dr. Vikki Petersen, a Chiropractor and Certified Clinical Nutritionist is co-founder and co-director, of the renowned HealthNow Medical Center in Sunnyvale, California. Acclaimed author of a new book, "The Gluten Effect" - celebrated by leading experts as an epic leap forward in gluten sensitivity diagnosis and treatment. Dr. Vikki is acknowledged as a pioneer in advances to identify and treat gluten sensitivity. The HealthNOW Medical Center uses a multi-disciplined approach to addressing complex health problems. It combines the best of internal medicine, clinical nutrition, chiropractic and physical therapy to identify the root cause of a patient's health condition and provide patient-specific wellness solutions. Her Web site is:

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