How To Spot And Heal A Child’s Leaky Gut

leaky gut in children

If your child is facing puzzling and recurring health challenges that are not medically explained, and you are tearing your hair out, knowing that things are somehow not quite right, then you might want to investigate whether they have gut permeability, also known as leaky gut.

From persistent tummy troubles to the more far-reaching aspects of their wellbeing, the effect of a compromised gut can touch all corners of child health and development. But we have had so many clients who were baffled with odd symptoms and doctors who couldn’t explain them either; and were so relieved when the test results came back with an answer they could act on.

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What is leaky gut?

Leaky gut is not well known amongst the general population or medical profession, despite there being over 7,000 scientific papers citing its importance.

Leaky gut occurs in the small intestine which is a very long winding tube that links the stomach and the large intestine. It’s where our body does all the hard work of digesting and absorbing food so your child gets all the benefits and nutrition from what they eat.

A healthy gut filters digested food matter via tiny finger-like projections called “villi”. These absorb beneficial nutrients and pass them out into the blood vessels surrounding the small intestine.

In between these villi are tight junctions which play a role in keeping toxins, pathogens and food bulk from getting through to those blood vessels. These tight junctions serve as the body’s security guards, preventing nasties from entering the rest of the body while allowing essential nutrients to nourish the cells through the bloodstream.

The tight junctions can be damaged quite easily either in the short term or the long term and become porous or no longer tight. One way to visualise leaky gut is to think of a long tube with tiny little holes in it. Leaky gut is when these the junctions allow the larger and unwanted particles like food particles, infections and toxins to escape into the blood stream. The body then goes into high alert mode and multiple symptoms, as described below can potentially occur. The presence of gut permeability over time can affect both the child’s immune system as well as the neurological system.

Why do kids get leaky gut?

Gut permeability is commonly caused by an overgrowth of unwanted pathogens living in the gut, which may include parasites (parasitic worms and/or amoeba), bacterial infections like salmonella, fungi (yeasts) and viruses. In my clinical experience it is rarely just one pathogen that causes the havoc, but more often it is a build-up of several unwanted gut bugs over time. When the bad bugs are in an environment where they can proliferate and colonise, they overpower the good bugs and the balance swings from mainly good bugs to mainly bad bugs in the gut microbiome.

Sometimes this is purely due to exposure to an infection that is not adequately addressed by the immune system or may be due to a build-up of exposure to milder infections such as from day-nursery or school settings. Antibiotic or proton pump inhibitors used for reflux either by the mother during pregnancy/breastfeeding or when given directly to the baby or young child, are scenarios often associated with the development of a leaky gut.

Repeated courses of antibiotics may make leaky gut more likely. This is because antibiotics are usually non-selective and can wipe out the beneficial bacteria at the same time as the infection. When the balance of bacteria is wrong, it may also trigger systemic yeast infections which may cause villi junctions to become leaky. Heavy metal and pesticide exposure can make these holes in the gut stay open for longer.

A diet high in refined sugars and white flour may be part of the picture in the onset of leaky gut. This is mainly because they can feed the “bad bugs’ which in turn promotes gut permeability.

Eating large quantities of ultra-processed food that contain additives such as emulsifiers, preservatives, and acidity regulators will not help. Additives are now very common in many convenience foods, sliced breads, processed dairy products, as well as some plant-based meat and dairy alternatives. These ingredients are thought to promote gut inflammation and gut permeability.

Some people acquire gut permeability when they have a histamine intolerance, which means that histamine naturally occurring in normally healthy foods such as tomatoes, oranges, avocado and spinach is not broken down effectively and the excess histamine in the gut can create gut permeability which might lead to allergy-type symptoms such as hives, itchy skin, flushing and feeling very hot at night.

Stress plays a big role in the development of leaky gut, and a person in a permanent state of “fight or flight” as opposed to “rest and digest” may also find it harder to heal their gut permeability.

Excessive exercise may also bring on leaky gut and could be partly why some very fit teen athletes succumb to post-viral illness or develop symptoms associated with gut permeability.

What effect can leaky gut have on a child’s health?

The effect of gut permeability can be far reaching and here is a bit more explanation.

The bad bugs such as bacteria, yeast and parasites that can cause leaky gut need to feed themselves to proliferate and thrive, and this means that they can act in a parasitic fashion stealing the nutrients from the food eaten by the child such as zinc and iron. This means that there is not much left in reserve to nourish the child’s body and brain. As you can imagine, this has a knock-on effect with their immune system and wellbeing and might explain why some children struggle to recover from viral infections compared to their siblings or peers.

Leaky gut can often be identified as a significant factor contributing to the development of various atopic and allergy-related issues in children, including allergies, food intolerances, chemical sensitivities and skin conditions like eczema and acne.

Additionally, it may play a role in issues such as early-onset autoimmune conditions, migraines, asthma, and adrenal problems which manifest as either persistent fatigue or feeling constantly wired.

The majority of our neurotransmitters (serotonin, dopamine, norepinephrine, acetylcholine and GABA), which help with mood and stress control, are made in the gut. Once the gut has been damaged there is a greater chance of fewer neurotransmitters being produced so things can worsen. Consequently, a child’s brain and nervous system cannot function properly, which can be part of the picture in the development of a huge array of neurodevelopmental and mental health outcomes.

It can also be part of the picture in mental health, behavioural and learning challenges, including depression, anxiety, obsessive-compulsive disorder (OCD), eating disorders, self-harm and suicidal tendencies. Additionally, it can be associated with neurodevelopmental differences such as autism, ADHD and sensory processing disorder, as well as behavioural challenges like ‘naughty’ or oppositional children, as well as learning differences such as dyslexia and dyspraxia.

How to spot leaky gut in kids

It’s not easy to tell if leaky gut is part of the picture, but here are some key symptoms that may warrant further testing:

  • A bloated or windy tummy, often with a skew towards irritable bowel, undigested food, diarrhoea or constipation.
  • Chronic gut pain, especially if it is above or around the belly button.
  • Ongoing reflux, especially if proton pump inhibitors like omeprazole or lansoprazole have been prescribed.
  • Changes in a child’s energy, mood or demeanour, which comes on after a bacterial or viral infection, or if a course of antibiotics have been taken orally.
  • Symptoms started shortly after a significant gastric upset (vomiting/diarrhoea) or parasitic infection.
  • Red ears or red rashes anywhere around the body, but particularly around the mouth and cheeks. These can be hives or eczema-type rashes or rashes that wax and wane.
  • Multiple food intolerances and allergies or histamine intolerance/mast cell activation.
  • Exacerbation of environmental allergy symptoms such as itchy eyes, runny nose, swelling, breathlessness or wheeziness. Exposure to mould or mycotoxins can exacerbate things.
  • Any auto-immune diagnosis as a combination of genetics and leaky gut seems to kick-start autoimmunity.
  • Skinny kids who have trouble growing and absorbing nutrients. Difficulty extracting the nutrients from the food they are eating, despite an excellent diet.
  • A child who is volatile, unpredictable, with anger or anxiety issues who easily get “hangry”.
  • Learning differences or neurodiversity may also be present alongside brain fog, easily zoning out and poor understanding of simple instructions.
  • A child or teen fixated on certain foods containing wheat/gluten or milk/dairy products like cereal, pasta, toast, crackers, yoghurt or cheese. See below for more information on opioid peptides which can lead to very narrow food choices.
  • Extreme food cravings for sugary and salty food as well as ultra-processed convenience food.

As you can see, these indicators could also be due to many other things, so it is important to carry out proper laboratory testing if a leaky gut is suspected.

Why can gluten, dairy and soya be an issue for some kids?

Some children do not produce enough Dipeptidyl peptidase IV (DPP-IV) enzyme to digest some of the proteins in foods containing gluten (wheat, rye, barley, spelt and some oats), as well as casein (all dairy products except ghee/clarified butter) and soya (tofu, tempeh, edamame or soya sauce).

This lack of enzyme production can be genetic or can be acquired through damage to the gut and will lead to these proteins being only partially digested, where they are then at risk of not being properly identified correctly by the gut immune system. When these proteins then escape into the bloodstream via the junctions between the villi, the systematic immune system has a hard time recognising them. This is partly because they aren’t where they are supposed to be due to the leaky gut.

Sometimes these partially digested proteins can reach the brain causing an opioid effect. Typically, a child with this issue is one who will only eat almost exclusively wheat and milk products (often cereal and milk for breakfast, a cheese sandwich for lunch, and pasta with butter and cheese for supper with yoghurt for pudding!) and also has behaviour/focus/attention problems (zoned out), speech and communication delay and/or poor social skills. This opioid issue can easily be tested for with a simple urine sample via our NatureDoc clinical team.

Long-term ingestion of too much gluten may be another reason for leaky gut. Alessio Fasano at University of Maryland discovered a substance called zonulin which controls the permeability of tight junctions in the gut. Gliadin (present in wheat) activates zonulin signalling and can lead to increased intestinal permeability, and this is why chronic gluten exposure may lead to leaky gut even in the absence of a coeliac disease diagnosis. A stool test can identify if zonulin is a problem for your child.

How to heal your child’s leaky gut

To improve your child’s gut permeability, you can follow this sequence, known as the 5R protocol. Take one step at a time and normally allow at least 6 weeks for each of the ‘R’ stages. Young children tend to bounce back faster than older teens, which means that the process can be sped up considerably, especially in the more robust kids with acute issues:

  • Remove residual pro-inflammatory bacteria, viruses, amoeba and yeast overgrowth using herbal or other natural antimicrobials. Also, remove any known food allergens or food intolerances. Remove sugar-sweetened drinks, foods containing white flour and refined sugar. Avoid food additives, especially emulsifiers and acidity regulators and switch to eating food cooked from scratch where possible. Infections in the gut can be identified through stool testing and/or organic acid/amino acid testing. Food intolerance testing and/or gut permeability testing can also be organised through a NatureDoc practitioner.
  • Replace the engines that aid proper digestion and absorption, such as pancreatic enzymes, hydrochloric acid and bile acids. Adding in plenty of lemon juice and apple cider vinegar and bitter salad leaves, as well as chewing food properly can make a good start.
  • Re-inoculate with beneficial bacteria to optimal levels using live yoghurt/kefir and probiotics as well as broadening the diet to include a wide range of fruits/vegetables, nuts, seeds, pulses and whole grains.
  • Recharge with nutrient-dense foods and choose good quality food supplements to replace any lost vitamins, minerals and amino acids.
  • Repair the gut with n-acetyl glucosamine or apple pectin and the amino acids glutamine, threonine, proline and serine. Soothing healing herbal blends such as slippery elm, marshmallow root and aloe vera can also be used. Include collagen-rich bone broths/meat stocks in stews, soups and add marine collagen to herbal teas, smoothies and yoghurt.

Round Up

As you can see there are many issues surrounding leaky gut, and healing a leaky gut can be complex. If you would like to run a stool or urine test to establish if your child does have leaky gut, then please be in touch with our Children’s Health Clinical Team who can create a health plan for your child’s specific gut health needs. They will create an individualised 5 Rs approach to help your child with their gut healing journey.

[The blog was first written in July 2015 and was updated on 12 November 2023]

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  1. Great blog piece, Lucinda – vigorous exercise can also temporarily increase gut permeability in adults so some opt to refrain from eating, specifically foods containing gluten, afterwards. Would this be the same for children?

    1. Hi Rayne. Yes vigorous exercise can trigger temporary gut permeability in both adults and children. If your child is competing in a triathlon or all-day rugby tournament then it would be prudent to give them a gluten-free post exercise lunch. I suspect however this would not apply after a big run around in the garden!

  2. This story reminded me of how I finally healed my leaky gut after years of agony. My life used to be miserable. I had chronic constipation, painful headaches, and acne that was out of control. The bloating and inflammation almost ruined my career, since I am a dancer and personal trainer. Needless to say, it doesn’t help to look less than fabulous in my line of work! I tried everything – including expensive supplements and so-called “healthy foods” that actually ended up causing more inflammation. I wondered if I would have to spend the rest of my life suffering and totally miserable. I knew that there had to be another way. I searched long and hard and finally came across some simple natural remedies that finally got rid of my leaky gut for good…to the amazement of my doctors. Hope it helps anyone reading this!

      1. Any kind of gut-based programme does take time and you do need to follow the 5 R’s to achieve this. You may well need to do a stool test to establish the most optimal support to help him get back on track. Many thanks Lucinda

    1. Hi anne, could you please share with me what were the simple natural remedies u did to heal your leaky gut. I have boys with behavioural issues and am looking at leaky gut as a big culprit. Thanks Marnie.

    2. I have an autistic son who is nonverbal and I want t start by testing his stool. Is there anywhere in uk who can test for leaky gut/peptides so toxins enter bloodstream/brain. Also test for parasites, yeast overgrowth, dysbosis etc. I’m thinking if tests prove he doesn’t have leaky gut I won’t need to put him on gluten/casein free diet. Can a good probiotic heal leaky gut? He’s 7. Thankyou

    3. Hey I have a daughter that poorly go’s to Dr.s and Drs with good allergies skin issues etc, and I’ m think the reasons is the leak gut.
      I came a cross to this article and your comment pls let me know what Dr. you find to help you to get treat???? I’m in USA have being in several Dr. office they not listen to me and my concerns
      Which type of Dr should I look for a cild 4 years old has being suffering since she was 7 moths older.
      Pls if you can help me I really appreciate.

      1. Hi there – unfortunately we cannot see kids in the US, so please seek out a paediatric functional medicine practitioner over there who will be able to help.

  3. Can you advise how you go about getting a stool test? My almost 7 year old daughter has been having gut issues now for around a year. I am not really getting much help from my GP. Is there a reputable firm I could use. I am based in Glasgow in Scotland.

    1. Hi Matilda. Thanks for your message, and I am so sorry your daughter has been having ongoing gut issues. Most people arrange an appointment through a Naturopath or Nutritional Therapist to discuss their child’s issues first. During the consultation the practitioner will advise on diet and supplements and also arrange the appropriate stool test to be sent. Results turnaround in about three weeks, so the practitioner will arrange a follow up for this time frame to discuss the results. All our NatureDoc practitioners offer Skype consultations if travel is an issue and I am sure would be able to help find the root cause of your daughter’s issues. Many thanks Lucinda

  4. Hi Lucinda; My 2.5year old has had chronic diarrhea now for a year after a bad GI infection our family got. I’ve had stool tests done and nothing shows up, she doesn’t complain of pain and she’s growing fine. What can I do for her? Her stool ranges from soft to watery and very rarely gets firm.

    1. Hi Pari. It sounds like she may need some gut healing support and many of the strategies such as probiotics and bone broths may be helpful here. She may have developed an a food intolerance after this infection so it would be worth looking into this. You may want to book in to see one of our NatureDoc practitioners if this continues.

  5. Hi – my 17 year old daughter went travelling last year and came back with bloating and constipation – after extensive tests and just recently 3 weeks in hospital she is now on a feeding tube and diagnosised with gastroparesis and unable to tolerate any food- is this something you could help with?

    1. Hi Sally. We do have experience with gastroparesis and one of my team would be very happy to help. Please call NatureDoc reception on 020 3397 1824 to book in. Best wishes Lucinda

  6. Hi
    I have a baby of two years old she is been suffering from eczema since seven months. I should say from her birth but it was coming very little and going by itself cuz I use coconut oil since she bron but from last seven months it’s not going it is becoming more worse day by day have checked with many doctors they say she has a very dry skin conditions and given us creams to apply they also gave us steroids too I used them but made her skin conditions more bad now I have stop using any steroids and using seba meds creams in her skin eczema goes but again Comes don’t know the reason why but I m totally worried and fed up too seeing her scratching all the time and yes she is super active kid moody too

    Plz help me plz

  7. I have a question, my kids and I had exposure to black mold in the hone for years. All of us have leaky gut including my 1 year old baby. What can we do about this?

    1. Hi Elizabeth. Thanks very much for your message. You would need to book in with one of my practitioners for a family appointment as gut healing is complex, especially when different ages are involved. I hope this helps. Best wishes Lucinda

  8. Can a pediatrion diagnose and test for leaky gut in a 4 mo old? Is it common at this age with supplementing cow/goat milk based formula and or giving solids before they are ready? I’m guessing it rarely happen with exclusive BF. Is it the same as I b s?

    1. Sadly not – the concept of leaky gut/gut permeability has not got much beyond the research stage in medical testing, so you will need to seek help from a naturopath or nutritional therapist. We can run stool tests under one year old but usually recommended for the over one’s but we can help with probiotics etc from weaning.

  9. hi, would you be able to say how much glutamine should a 12 yo child be given to heal leaky gut? There is such a big discrapency between research studies (e.g. 0.3g/kg pd) and some recomendations given by nutritionists or glutaine supplement manufacturers (e.g. 1g pd only)… what is your suggestion? thank you

  10. This is an excellent article for a mom like me. You gave me more insights about having a healthy gut for my kids. I learned a lot from your writing. Thank you for this article!

  11. Hi Lucinda,
    Thank you for the very helpful and informative article! This is what I’ve been looking for!
    When applying the 5R protocol, is there any room for a piece of cake at a party or would that mess up the whole process?
    Thank you!

    1. In some cases it might set you back a few days – everyone is a little different – but the reality most people find it hard to stick with everything 100% – the beauty of some of the supplements is that these can help with the inevitable bumps along the way!