How To Spot And Heal A Child’s Leaky Gut

leaky gut in children

Leaky gut will be a new concept to many people, but it is super important to learn about gut permeability if you have a child who is not thriving right now, as this common gut issue could easily be the root of unexplained or apparently unrelated health issues. This article shares how to test for gut permeability and some top tips to tackle this very common problem which is now known to play a significant role in many far-reaching childhood physical and mental health conditions, as well as behavioural and developmental issues.

Sadly, there is no quick fix and the process to sort it can take time and it is important to follow the “5 R” approach. Those that do stick to this process will not only help their child with current symptoms but will probably help avoid developing something even more problematic in the future. In my experience with kiddie gut health and nutrition little niggles when they are young can potentially lead to greater issues when they are older, so it is worth getting their gut health in tip-top condition when they are tiny – but equally, it is never too late to work on gut health either and adults and teenagers will also benefit from the “5R” approach.

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How to spot leaky gut in kids:

It’s not easy to tell, but here are some key pointers that 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 foods as well as ultra-processed convenience foods

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

What is Leaky-Gut?
Leaky gut is on the rise in both children and young adults and is now featured heavily in scientific literature. Naturopaths, nutritional therapists and functional medicine practitioners often find that this is an important piece in the puzzle of why children develop allergies, food intolerances, chemical sensitivities, skin conditions such as eczema and acne, low immunity, early-onset autoimmune conditions, migraine, asthma, adrenal issues (tired and wired or exhaustion). It may also be why a child does not recover from a viral infection as easily as their siblings or peers.

It can also be part of the picture in mental health, behavioural and learning challenges to include depression, anxiety, obsessive-compulsive disorder (OCD), eating disorders, self-harm, suicidal tendencies, neurodevelopmental differences such as Autism, ADHD and sensory processing disorder, as well as behavioural challenges such as “naughty” or oppositional children, as well as learning differences such as dyslexia and dyspraxia.

Your small intestine is a very long pipe that links your stomach and your large intestine and filters digested food matter via tiny finger-like projections called “villi”. These absorb beneficial nutrients and pass them out into blood vessels surrounding the small intestine while keeping toxins, pathogens and food bulk from getting through to those blood vessels. They are the guts security guards who prevent nasties from being transported into the rest of the body and let the good guys in to feed the blood and ultimately nourish the cells. In that sense, the small intestine is supposed to leak the good stuff into the bloodstream, and it all goes wrong when the filter isn’t fine enough and the bad stuff gets in too.

The villi are normally very closely packed together, but leaky gut occurs when junctions between them are no longer tight and allow the larger and unwanted particles to escape into the blood vessels.

Why are gluten, dairy and soya such an issue for some kids?
Partially-digested proteins, known as “peptides” are especially at risk of not being properly identified correctly by the gut immune system. When these proteins, such as gluten, casein (milk) and soya, escape into the bloodstream before being broken down properly, the immune system has a hard time recognising them. This is partly because they aren’t where they are supposed to be. It often sends signals to the immune system to flag the partially-digested foods as allergens or food intolerances. Once the immune system has flagged a substance, it remembers it as an enemy and will react the same way each time there is an exposure.

In other circumstances 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 via a simple urine sample.

Another trigger may be long-term ingestion of excess gluten. Alessio Fasano at University of Maryland discovered a substance called Zonulin that 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.

Anyone recently diagnosed with coeliac disease (an autoimmune reaction to gluten) will have had compromised villi health which leads to gut permeability. A strict gluten-free diet needs to be adhered to for life and the ‘5 R” approach can potentially help the villi to heal faster.

Why does leaky gut occur?
This is commonly caused by an overgrowth of unwanted pathogens living in the gut, which may include parasites (parasitic worms and/or amoeba), bacteria, fungi (yeasts) and viruses. In my clinical experience it is rarely just one pathogen, but more often a build-up of several unwanted gut bugs. When the bad bugs are able to proliferate and colonise, they overpower the good bugs and the balance swings from mainly good bugs to mainly bad bugs.

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 in day-nursery settings. This is why it is so important to do stool testing to get a grip on what is causing havoc to your child. Antibiotic or proton pump inhibitor use for reflux either by the mother during pregnancy or breastfeeding or given directly to the baby or young child is 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. What does not help is eating large quantities of ultra-processed food that contain additives such as emulsifiers, preservatives and acidity regulators, which are now very common in many convenience foods, sliced breads, processed dairy products, as well as some plant-based meat and dairy alternatives.

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” also may find it harder to heal their gut permeability. Excessive exercise may also bring on leaky-gut and may be partly why some very fit athletes succumb to post-viral illness or develop symptoms associated with gut permeability.

Why is leaky gut so detrimental to your child’s health?
The majority of our neurotransmitters (serotonin in particular) and 70-80% of our immune system are made or located in the gut. Once the gut has been damaged there is a greater chance of fewer neurotransmitters being produced and the immune system running low or misfiring. As a consequence, our brain, nervous and immune systems cannot function properly, which can cause this huge array of health conditions.

Most of our food these days is very complex. It contains all sorts of emulsifiers, acidity regulators, colours, preservatives, artificial sugars, and may even be “enriched” with synthetic vitamins. Even our “fresh foods” could be contaminated with pesticides, hormones, antibiotics, or contaminated groundwater. This tends to further confuse the system and these specific toxins and additives may also be tagged as enemies. If the body detects anything that it thinks is an enemy, it will try to reject or dump everything you have eaten recently, including all the good stuff.

This “dumping” may explain why so many kids need high doses of additional nutrients despite eating a “healthy diet”. And since the bad bugs tend to steal the nutrients anyway, there is often not much left to feed the child’s body and brain. If the gut has been severely damaged, it will struggle even to absorb the basics, so to heal it, we generally use capsules, liquid or powdered food supplements and sometimes vitamin skin patches, which work better than tablets, as they are easier to break down and absorb.

How to heal your child’s gut – the 5 Rs

To improve your child’s gut permeability, then it is important to follow this sequence – take one gut-healing step at a time and normally allow at least 6 weeks for each “R” stage – young children do tend to bounce back faster than older teens, and sometimes the steps can be done together which means that the process can be sped up considerably, especially in the more robust kids with more 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.

[The blog was first written in July 2015 and was updated in March 2022]



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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!