How to Detect and Address Gut Issues in Autism

Published article in the Autism Eye Magazine December 2021 written by Stella Chadwick

Multiple studies have shown that, children with autism are more prone to gastro-intestinal (GI) problems and in 2014 a study found that these children were four times more likely to have symptoms such as constipation, diarrhoea, or other GI symptoms.  A 2017 study based on almost 300,000 children with autism revealed that they are almost 70% more likely to have the diagnosis of IBD (irritable bowel disease). GI symptoms can manifest as picky eating, sensory processing issues, meltdowns, head-banging, aggression, self-harming, as well as poor weight gain and poor muscle tone. The connection of these symptoms to GI issues can be especially hard to ascertain if the child is nonverbal.

The impact of comprised gut health on the brain is also well documented and we know that we have more neurotransmitters in our gut then we do in our brain. About 95% of serotonin is produced in the gut. Serotonin is our feel-good neurotransmitter and is the precursor to melatonin our sleep hormone. That is just the tip of the iceberg. Having worked with thousands of children on the spectrum in our clinics we know first-hand how life changing getting a healthy gut can be for these children. We have seen tremendous positive impact on sleep, mood, behaviour, focus and attention, socialisation, and speech.

In this article we will look at the most common symptoms we see in our clinic and help empower you to advocate for detailed investigations into the health of your child. If your child has had prolonged symptoms which have lasted more than a few weeks, then it is imperative that they are seen by a paediatric GI consultant. The key symptoms of compromised gut health are outlined in Table 1.



Constipation is complicated and very common in children on the autism spectrum.  What may surprise you to know is that children can be constipated even if they have daily bowel movements. This is because even though the bowels are opening daily the child is simply not excreting enough stool. Please pay attention to the texture of the stool which should be soft and easy to pass, as well as the frequency of bowel movements which should occur at least once a day. The amount of stool expelled is also very important and doctors generally suggest 8 to 10 inches of stool per day as a good measure that the bowel is emptying adequately. The Bristol Stool Chart in this article can help guide you as to what a good quality stool should look like.


There are multiple reasons for constipation, including poor hydrochloric acid (HCl) in the stomach (very common especially in those with a history of multiple rounds of antibiotics and other medication), lack of enzymes due to pancreatic insufficiency, food sensitivities especially to gluten, dairy and soya, celiac disease, inadequate water and fibre intake, muscle, or nerve damage (usually due to long term constipation where the bowel has been stretched), gut dysbiosis because of out of balance gut microbiome, ileocecal valve problems, straining and impaction. Certain supplements like iron and calcium, or binders like activated charcoal or chlorella, or yeast-based probiotics like saccharomyces boulardii, as well as medications like antacids, certain anti-depressants, calcium channel blockers, pain medication like ibuprofen and paracetamol, overuse of laxatives, anti-psychotics like aripiprazole, and ADHD drugs like risperidone can all contribute to constipation. You can find out more about constipation in children with autism and how to help them in the Autism Eye summer 2017 edition.



Prolonged diarrhoea can be a serious medical matter and must be investigated by your medical team. Since the stool moves really fast the nutrients from food consumed do not have the chance to be absorbed properly and these children become nutrient deficient and fail to thrive. Things don’t always have to be too complicated, and you should make sure that your child is not having too much fruit (1-3 portions a day should be tolerated in a normal healthy gut), or too much fibre. In terms of supplements, magnesium, vitamin C and fish oils can have a diuretic effect. A lot of parents use Epsom salts in the baths. Children who regularly drink the bath water containing these salts may be prone to loose stools. Food sensitivity is also extremely common especially to dairy, artificial sweeteners also known as sugar alcohols such as sorbitol (E420), mannitol (E421), isomalt (E953), maltitol (E965), lactitol (E966), xylitol (E967), and erythritol (E968) found in so called “healthy” sugar free foods and drinks as well as hydrogenated fats found in many baked goods and crisps and roasted nuts and seeds. Some children are particularly sensitive to food high in FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) which are a group of sugars that are not completely digested, causing overproduction of gas, leading to bloating and diarrhoea. High-FODMAP foods include sugar alcohols and lactose; fructose, which is in higher concentration in some fruits and honey; and fructans and GOS-containing foods such as onions, legumes and wheat. Using functional stool tests for our patients we have found a strong connection between chronic diarrhoea and overgrowth of pathogenic organisms in the gut, such as clostridium difficile, parasites, and several species of yeast causing significant inflammation in the GI tract.



This is a very serious and often painful condition where the stool has backed-up in the colon and has become a mass and appears to be stuck in the colon. Due to the nature of the mass, it might be that your child has what looks like loose bowels as some of stool can get squeezed passed the mass and look like diarrhoea or thin ribbony stool. Key signs are alternating dialarhoea and constipation, low output of stool, with bowels never seeming to empty properly, bloated tummy, chronic disturbed sleep, poor appetite, aggression, and hyperactivity. If you suspect impaction, please make sure your child is referred to a GI consultant. Usually, an abdominal Xray is necessary to confirm the backed-up mass in the colon.



This can start as a baby and continue undetected for many years. Untreated prolonged acid reflux can burn the oesophagus and cause a lot of pain. This is especially problematic for non-verbal children and needs to be thoroughly investigated. These children tend to be very picky eaters and can be aggressive, have meltdowns and self-harm regularly.


Enzyme deficiency

The two most common functional tests we complete for our patients are a urine organic acid test and a comprehensive stool analysis. Through these tests we often find problems with enzyme activity as well as Pancreatic insufficiency, as determined by reduced faecal elastase-1 levels (<200 μg/g stool), although 1 in 2 cases can be missed if using this as the only marker to consider. Pancreatic insufficiency can often be accompanied by serious conditions such as Crohn’s disease, ulcerative colitis, and can be driven by cow milk allergy, high levels of gut pathogens, coeliac disease or non-coeliac gluten intolerance, as well as conditions like diabetes. These conditions are almost always accompanied by high levels of inflammation. In many cases removing problem foods and clearing gut pathogens and replenishing the microbiome and using enzymes can help reverse some of these symptoms. In all cases it is crucial for your medical team to thoroughly investigate the underlying biochemistry.


Other underlying health issues contributing to GI Symptoms

Sometimes there are more complicated issues at play contributing to poor gut health. The most common issues are mitochondrial dysfunction and dysregulated thyroid function which can both contribute to unresolved constipation. To get an overview of mitochondrial function a urine organic acid test like the one by Great Plains Laboratory which you can order from Biolab medical unit in London would be a good place to start. Ideally your medical team should consider checking lactate, plasma amino acids, urine organic acids, carnitine – frozen plasma and blood ammonia. A more detailed and cutting-edge test to get a detailed picture of the health of the mitochondria can be done through a saliva test called the MitoSwab, which we offer to our patients. In terms of thyroid function, it is not enough to simply measure TSH and T4. It is imperative that you measure free T3 and free T4, reverse T3, and thyroid antibodies, including thyroglobulin antibodies and thyroid peroxidase. Without a complete picture the state of the thyroid cannot be assessed adequately. This investigation is particularly important if there is a history of thyroid dysregulation or thyroid disease in the family health history.


Table 1
Key GI Symptoms
Chronic constipation or diarrhoea
Foul smelling stools with odd texture and colour
Distended tummy
Undigested food or signs of mucous in stools
Poor muscle tone and poor weight gain
Extreme picky eating
Inability to be potty trained past a reasonable age
Unexplained aggression, meltdowns, and self-harming
Posturing behaviour by leaning over objects like the arm of a sofa or a yoga/therapy ball for example
Bed wetting
Extreme sleep issues


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