Why You May be Feeling Worse After Going Gluten Free

If you are feeling worse after going gluten free there are some other medical considerations that should be investigated as to why you may not be feeling better.

For those with celiac disease and gluten intolerance, following a gluten free diet is a must. We often tell our patients the timeframe to start feeling better is 3-6 months. If they still don’t feel better on the gluten free diet within this time period, we start to look deeper into the common complications that can coexist with gluten intolerance and celiac disease.

In our experience, if you are feeling worse after going gluten free, the complications that should be looked into include:

  • Malabsorption and nutrient deficiencies
  • Prolamine intolerance to foods that are cross-reactive with gluten
  • Yeast in the gut – intestinal candidiasis
  • Leaky gut syndrome
  • Endocrine problems
  • Diamine oxidase deficiency and food allergies

Each of these complications is explained in greater detail below.

Malabsorption is the inability to absorb nutrients from food. This is of specific concern for those with gluten intolerance or celiac disease, the key vitamins and minerals that should be monitored via blood work are:

  • B12 deficiency: can cause fatigue, brain fog, concentration problems, and anemia
  • Biotin deficiency: can cause hair loss and brittle nails
  • Zinc/Copper deficiency: can cause eye and mouth dryness, abnormal liver function, and poor wound healing
  • Iron deficiency: can cause fatigue and muscle weakness
  • Vitamin D deficiency: can cause cramps, osteoporosis, and pseudogout
  • Magnesium deficiency: can cause constipation, and cramps in legs and muscles
The good thing is these deficiencies can be easily solved by taking the corresponding dietary supplement. Based on your lab results, your doctor will recommend taking the supplement to eliminate the deficiency.

Foods that are cross reactive with gluten

Gluten is a part of a large group of proteins called prolamines that are extremely resistant to degradation by our digestive system.

Because this group has molecular similarities to each other, it is highly possible that if you are intolerant to one, you may be intolerant to the others as well.

These items are:

  • Casein from cow’s milk
  • Soy
  • Albumin in egg whites from chicken
  • Corn


Typically casein from cow’s milk causes the most problems for people, based on our clinical experience; approximately 60-70% of people who are gluten intolerant are also intolerant to casein. Goat’s milk and sheep’s milk do not cause the same problems as well as plant based milks like almond or coconut.

dairy products


50% will be intolerant to soy. When it comes to soy, the problem comes from ingesting soy protein. Typically problems do not occur with soy lecithin as lecithin is a highly extracted product with very minimal protein remaining.

 shelled soy beans


15-20% intolerant to albumin in egg whites from chicken. Duck and quail eggs are safe to consume.

stack of eggs


10-15% will have a problem with corn.

One thing to note, you can be gluten intolerant  AND prolamine intolerant where all of these items will cause problems and should be eliminated from your diet. Roughly 15-25% of the celiac disease and gluten intolerant population are prolamine intolerant.

corn stalks

How do you know if you are prolamine intolerant?

The best way to figure out of you are prolamine intolerant is to eliminate the items listed above one-by-one and pay attention if you begin to feel better.

Yeast Overgrowth

Candida albicans is an acceptable part of normal intestinal microflora. But under certain circumstances, candida starts to overgrow and occupies more space in the gut than should be and becomes harmful—this condition is commonly known as yeast overgrowth or candidasis.

Yeast exists in two forms, round and hyphae. Round forms do not present any harm, the hyphae, or budding form are much more invasive producing toxins and over stimulating the immune system.

Symptoms of yeast overgrowth in the gut include:

  • Craving for sweets
  • Bloating
  • Acne
  • Postprandial fatigue—wanting to sleep soon after eating (20-30 minutes)
  • Migraine headaches
  • Hives
  • Eczema

The overgrowth can manifest in several ways including thrush, chronic yeast infections, or skin rashes. Thrush is a yeast infection in the mouth that is typically characterized by a white coating on the tongue. Yeast infections are often found in women as vaginal yeast infections. Skin rashes manifest as red, inflamed areas typically in warm areas such as underarms.

What causes yeast overgrowth?

Candida overgrowth is frequently seen in individuals with gluten intolerance and celiac disease, those who frequently use antibiotics, non-steroidal anti-inflammatory drugs, steroids, hormones, and birth control pills (studies have shown that yeast feeds on estrogen).

How to treat candida?

Candida can be difficult to get rid of because it forms a gel-like structure (biofilm) around itself, which prevents antibiotics and antifungal products from penetrating. Because of this barrier, candida can exist for months or even years.

When targeting candida, there are three things to keep in mind:

  1. Bring the yeast count under control
  2. Prevent hyphae formation
  3. Prevent biofilm formation

Keeping these 3 things in mind, along with following a low-carb diet, there are dietary supplements that can be used in the treatment of candida.

Goal  Solution
Stop feeding yeast Follow a low-carb diet

Digest food completely (left over food 
gets consumed by yeast)

Digestive enzymes

Normalize gut microflora (simulate good
microflora to suppress yeast)

Prebiotics and probiotics

Reduce yeast in the gut

Black Walnut Hulls, Pau D'Arco

Stop biofilm formation

Serrapeptase, Bromelain


What to do if you have signs of candida overgrowth?

The first step is to go on a low carb diet and take the recommended supplements.

Depending on the severity of overgrowth, you will need to follow this for at least 6-9 months; noticing a difference in 2-3 months.

If you have uncontrollable bloating, diarrhea, skin rashes, or a vaginal yeast infection it is time to see a doctor.

Leaky Gut Syndrome

Leaky gut syndrome is a well-defined functional disorder of the gut characterized by increased intestinal permeability.

What does this mean?
Imagine the gut as a hollow tube with walls built of billions of living building blocks (epithelial cells). The tube is inhabited by a myriad of microorganisms, some of which attach to the tube and others float within the lumen. In a cyclical way, the tube fills up with remnants of food, bile, and digestive enzymes and acts as a highly selective filter, or tight junction allowing only a small portion of molecules to escape the lumen into the bloodstream. When this filter is abnormal too many food bacteria and toxins are released into the bloodstream causing leaky gut syndrome.

The causes of Leaky Gut Syndrome are wide and varied, some of the main causes include:

  • Poorly balanced diet. Especially carbohydrates.
  • Chronic use of alcohol
  • Intestinal parasites
  • Chronic yeast (candida) infection
  • Abnormal gut microflora (dysbiosis)
  • Chemotherapy or radiation therapy
  • Prolong use of antibiotics
  • Chronic use of NSAIDs (ibuprofen, naproxen, diclofenac etc)
  • Chronic use of corticosteroid hormones prednisone
  • Chronic use of estrogens (birth control pills, hormone replacement therapy etc). As mentioned previously, yeast cells become more aggressive during high periods of estrogen levels.

Common symptoms of leaky gut syndrome:

  • Acne, hives, and eczema
  • Bloating and abdominal discomfort after eating
  • Brain fog
  • Diarrhea
  • Eating-associated fatigue, muscle weakness and pain
  • Mucus in the stool
  • Poor tolerance of alcohol—become drunk easily. (The sulfites in alcohol and can also increase leaky gut.)

Leaky Gut Syndrome Consequences

Leaky gut syndrome has been known to make the following conditions much more symptomatic. If the underlying leaky gut syndrome is not also treated, the therapy of your condition will not be as effective. 

  • Ankylosing spondylitis
  • Asthma
  • Autoimmune hepatitis
  • Celiac disease and gluten intolerance
  • Chronic fatigue
  • Chronic sinusitis
  • Crohn’s disease
  • Diabetes
  • Eczema
  • Hay fever
  • Migraine headaches
  • Psoriasis and psoriatic arthritis
  • Rheumatoid arthritis
  • Ulcerative colitis

Therapy of Leaky Gut Syndrome

In our clinic, IFSMED, we address leaky gut syndrome with dietary supplements.

Goals of therapy are:

Improve food digestion with digestive enzymes. Leftover food in our system gets consumed by yeast allowing the yeast to become more aggressive and overgrown.

Normalize gut microflora with probiotics. Our gut microflora is the community of microorganisms that live in our gut.

Optimize mucosal immune responses. With Mannan Oligosaccharides, Epicor, Black Currant Seed Oil, and Bovine Immunoglobulins. Our mucosal immune system provides us with protective mechanisms against invasion by potential pathogens while allowing normal intestinal flora to persist.

Restore tight junctions. With Probiotics, N-Acetyl Cysteine, and Sodium and Magnesium Butyrate

Common endocrine abnormalities in gluten intolerant individuals

The endocrine system is the collection of glands that produce hormones that regulate metabolism, growth and development, tissue function, sexual function, reproduction, sleep, and mood, among other things. It is made up of the pituitary gland, thyroid gland, parathyroid glands, adrenal glands, pancreas, ovaries (in females) and testicles (in males).

The link between gluten and the endocrine system is based on the ability of gluten to change (either inhibit or stimulate) the production of certain hormones, including thyroid hormones, testosterone, prolactin, and estrogens.

If you are feeling worse after going gluten free the following should be checked for abnormalities:

  • DHEA/DHEA sulfate deficiency
  • Hashimoto disease of thyroid gland
  • Hypothyroidism
  • Insulin resistance
  • Overproduction of prolactin causing menstrual irregularities
  • Pregnenolone deficiency
  • Polycystic ovaries
  • Testosterone deficiency

Diamine (histamine) oxidase (DOA) deficiency

DOA is an enzyme that controls the inactivation of histamine. A DOA deficiency is common in those with gluten intolerance and celiac disease and the cause of elevated histamine in this population. It is also a reason why those with gluten intolerance and celiac disease are sensitive to a variety of foods.

Here are the basic steps of how histamine and DOA work after we eat and what happens in those individuals that are DOA deficient.

The normal physiological process of histamine and DOA

When we eat our gut releases histamine.

Histamine opens up our blood vessels to allow food to get absorbed in our body.

At the end of this cycle our body releases the DOA enzyme.

DOA breaks apart histamine causing blood vessels to collapse and absorption stops.

What happens if you have a diamine oxidase deficiency?

After you eat your body doesn’t release DOA, so histamine lasts much, much longer triggering leaky gut, hives, itching, headaches, upset stomach, and allergic reactions.

What to do if you are DOA deficient?

The good thing is DOA can be stimulated by taking supplements.

Two that we readily recommend are:
DOA supplement from pig kidneys and Bioflafonoids

You can also consider following a histamine-free diet, but it is very restrictive and difficult to follow, much more than a gluten free diet.

For those who are gluten intolerant or have celiac disease following a gluten-free diet is a requirement to feeling better. For many in this population, following the diet is enough to help ease their symptoms. If you are gluten-free and still feeling sick, your doctor should check for the reasons covered above as possible contributors to your malaise.

Cover photo: Photo by Ivan Aleksic on Unsplash