Gut health tests for children: which ones are useful?

Written and clinically reviewed by Bahee Van de Bor, RD, BCAPSc PGDipDiet, Specialist Paediatric Dietitian, former specialist dietitian at Great Ormond Street Hospital, with over 20 years of clinical experience in paediatric nutrition.

Last reviewed: 11 November 2026

“Is there an accurate gut health test for my child?”

I know this question comes up when you are worried and bewildered by your child’s loose stools, or by constipation that persists and that no one has been able to explain.

You’ve done everything you were asked to do, and your child still has tummy pain or stools that aren’t right.

So you want someone to look inside and tell you what is going on, and plenty of companies will sell you a kit that promises to.

This guide is for parents of otherwise well children with ongoing tummy pain, constipation or loose stools.

Here is what each test can tell you, what it can’t, and which ones I would want for a child in the Happy Belly Club®.

Tests at a glance

Considering a particular test? Jump straight to it below.

• Coeliac screen (blood test): checks for coeliac disease; your child needs to be eating gluten for a reliable result.
• Calprotectin (stool test): checks for signs of gut inflammation; not recommended for constipation alone.
• Infection testing (stool test): looks for specific infections when ongoing diarrhoea and the history suggest one.
• X-ray and ultrasound (tummy scans): not routinely needed to diagnose constipation.
• SIBO breath test (hydrogen and methane): can help in selected cases, but a positive result doesn’t necessarily explain your child’s symptoms.
• Lactose and fructose breath tests: not routinely recommended for investigating functional tummy pain.
• Microbiome testing (stool kit): cannot reliably explain your child’s symptoms or identify the right treatment.
• IgG food intolerance testing (blood test): not recommended for identifying foods that cause symptoms.

What should happen before choosing a test?

An assessment comes first, because it decides whether any test is worth doing. Tests can be useful, particularly to rule out other conditions when your doctor suspects one.

That means the full story:

• when the symptoms started
• what the stools look like on the Bristol Stool Chart
• how often your child goes
• whether they hold on
• what they eat and drink
• how they are growing
• what you have already tried

Here’s what you need to know. A doctor can recognise functional constipation and IBS from the pattern of your child’s symptoms.

Rome V, the criteria specialists use worldwide, says constipation can be diagnosed from your child’s story and a physical examination.

Your child doesn’t need every other condition ruled out with tests first.

After the assessment, the question for every test is simple. Would the result change what we do next?

Which medical tests can help, and when?

A GP or paediatrician may arrange these when your child’s story gives a reason.

Each one answers a different question, so your child won’t necessarily need any of them.

Does my child need a coeliac blood test?

Your child may need a coeliac blood test if tummy symptoms keep going, because coeliac disease can cause ongoing tummy symptoms and poor growth.

The coeliac blood test only works if your child is eating gluten. NICE advises eating some gluten in more than one meal every day for at least six weeks before testing.

Cutting gluten down or out beforehand can make the result falsely reassuring.

So please don’t change your child’s gluten intake before you have spoken to your GP, and if you already have, tell them before the test is booked.

NICE also advises checking your child’s total IgA level alongside the coeliac test.

IgA is a type of antibody your immune system makes, and the usual coeliac test looks for a coeliac antibody of this type.

If your child’s IgA is low, the usual coeliac test can miss the condition, and the doctor will use a different one.

What does a calprotectin stool test show?

A calprotectin stool test shows whether there are signs of inflammation in the gut.

Calprotectin is a protein that shows up in stools when the gut lining is inflamed, and the test helps a doctor decide whether symptoms might come from an inflammatory condition, such as inflammatory bowel disease, rather than a functional gut problem.

Calprotectin isn’t a test for constipation alone. The ESPGHAN calprotectin position paper recommends against using it in constipation, and the Rome V constipation guidance doesn’t include it.

Healthy young children, especially under fours, can have higher calprotectin levels, so their results need age-appropriate interpretation by their doctor.

When does a stool test for infection help?

A stool test for infection helps when your child has ongoing diarrhoea and there is a reason to suspect a bug, such as recent travel or contact with someone unwell.

Your GP can send a stool sample to the lab.

On the form or results, you may see:

• MC&S (microscopy, culture and sensitivity): looks for bacteria
• OCP (ova, cysts and parasites): looks for parasites such as Giardia
• PCR: picks up the genetic material of several common bugs at once, and many labs now use it

Tummy pain that carries on after a stomach bug has cleared is a different picture, and a stool test usually won’t explain it.

I’ve written about gut problems after a stomach bug separately.

An infection test is also very different from the microbiome kits sold online.

An infection test looks for a specific bug that can be treated.

A microbiome kit describes which microbes are present, which is currently more useful in medical research than in your child’s personalised care.

Should my child have an X-ray or tummy scan?

Usually not, if the question is constipation.

NICE advises against using an abdominal X-ray or ultrasound to diagnose constipation in children.

A specialist may occasionally use them later, in the ongoing management of constipation that is very hard to treat.

Many parents ask why the GP won’t “just scan the tummy”. Scans don’t reliably show whether a child is constipated.

Rome V describes X-rays as neither sensitive nor specific for constipation, which means they can miss it and can suggest it when it isn’t there.

A careful history and examination by an experienced professional tell the doctor more. An X-ray also uses a small dose of radiation, so it’s best avoided when it won’t change the plan.

Does my child need a SIBO breath test?

A SIBO breath test has a place when a child has a clear medical reason for SIBO.

For an otherwise well child with tummy pain or constipation, I don’t recommend routine SIBO testing, or antibiotics on the strength of a private result.

SIBO stands for small intestinal bacterial overgrowth.

It means too many bacteria are living in the small bowel, the part of the gut that normally holds relatively few.

A breath test looks for it by giving your child a sugar drink and measuring the gases that gut microbes produce as they ferment it.

Doctors sometimes ask for my view after a private breath test has come back positive and antibiotics are already being planned.

So here is how I think about it.

When is a SIBO breath test worth doing?

Your child’s history decides whether a SIBO breath test is worth doing.

SIBO is a real problem in children with particular medical conditions.

These include short bowel after surgery, intestinal failure, cystic fibrosis, and rare conditions where the small bowel can’t move food along properly, such as chronic intestinal pseudo-obstruction.

SIBO symptoms are variable and overlap with other gut problems, according to the ESPGHAN expert review of SIBO in children.

They include diarrhoea, bloating, wind and tummy pain, so symptoms alone can’t tell you whether SIBO is there.

Weight loss or poor growth need a medical review in their own right, whatever the cause.

In an otherwise well child with tummy pain or constipation, what a positive breath test means is far less clear.

Is slow gut movement the same as constipation?

No. The slow gut movement linked to SIBO happens in the small bowel, which normally sweeps itself clean between meals.

When you read that “slow gut movement” causes SIBO, it sounds like constipation, and that causes a lot of confusion.

Functional constipation on its own doesn’t mean your child has a small bowel motility problem.

Is a SIBO breath test accurate in children?

A SIBO breath test is hard to rely on in children.

There is no agreed definition of SIBO in children, and the ESPGHAN expert review describes the evidence on diagnosis and treatment in children as lacking.

Breath test results also depend heavily on how the test is done.

The sugar used, how long the test runs, what your child ate the day before, recent medicines and how quickly food moves through the gut all change the reading.

So when a private test comes back positive in an otherwise well child, I’m still not convinced we know what that result means.

SIBO or constipation: what should come first?

In a constipated child, getting the constipation treatment right comes first, and a methane result on a breath test doesn’t change that.

If your child is constipated, you may have read that methane on a breath test means an “overgrowth” that needs antibiotics or herbal antimicrobials.

Methane is linked with slower transit through the gut. But the methane link doesn’t tell you which came first in your child, or that treating the methane will help.

A breath test isn’t a measure of how fast the gut moves, either.

In a constipated child, my priority is assessing the constipation and getting the treatment right, including clearing a backlog if there is one.

That is the step that changes how your child feels.

Does my child need to stop laxatives before a breath test?

Breath test preparation varies by service, and the testing service can tell you how to prepare for its test.

Please don’t stop or reduce a prescribed laxative for a test without talking to the doctor who prescribed it.

NICE advises against stopping laxatives abruptly, because the constipation can build up again.

I’ve written about why constipation comes back when laxatives stop too early.

Is SIBO testing available on the NHS?

Some NHS trusts offer breath testing for children, such as Addenbrooke’s paediatric gastroenterology, usually when there is a specific medical reason.

In my experience, an otherwise well child with tummy pain or constipation is rarely offered one, so the breath tests I see in these children have usually been done privately.

Are lactose and fructose breath tests useful for tummy pain?

Not routinely. For children with functional tummy pain, the ESPGHAN breath testing position paper recommends against using lactose and fructose breath tests routinely.

These tests look for difficulty absorbing milk sugar or fruit sugar, which is a separate question from SIBO.

The same paper warns that relief on a sugar-restricted diet after a positive breath test can delay a coeliac diagnosis.

Are home microbiome test kits worth it?

Not yet. A commercial microbiome stool kit can’t currently tell you what is causing your child’s symptoms or which treatment will help.

Changes in the gut microbes are real, and they matter.

As a member of the ESPGHAN Special Interest Group on Gut Microbiota and Modifications, I find this one of the most exciting areas of research.

The problem is the leap from the research to a kit.

An international consensus on microbiome testing found no agreed definition of dysbiosis and advised against reporting dysbiosis scores.

So the change in the gut microbes can be real, while a “dysbiosis” label from a stool kit isn’t a diagnosis.

Do food intolerance tests work?

No. IgG food intolerance tests aren’t recommended for finding foods that cause symptoms.

IgG food intolerance tests measure your child’s immune response to foods they have eaten.

A raised result mostly shows your child has eaten that food, which is what you would expect. I’ve covered them in detail in are food intolerance tests accurate?.

If your child’s doctor or dietitian suspects a delayed (non-IgE) milk allergy, a blood test won’t answer it either.

NICE advises diagnosing this type of milk allergy by removing milk for a trial period, usually 2 to 6 weeks, then bringing it back to see whether symptoms return.

Do this with your GP or a paediatric dietitian, so your child’s diet stays balanced while milk is out.

What if the results are normal, or a private test comes back positive?

If the tests are normal

Normal test results are useful.

They answer the specific questions they were asked.

Your child’s team can use the results alongside their symptoms, growth and examination to decide what to do next.

Your child’s pain can be real and persistent even when tests haven’t found an explanation.

One possible explanation is visceral hypersensitivity: the nerves in the gut become more sensitive, so ordinary stretching and movement can feel painful.

I’ve written more about this in tummy pain when tests are normal.

If a private test comes back positive

Before acting on a positive private test, ask three questions.

• Who will interpret this result alongside my child’s history?
• What treatment is being suggested, and is there evidence for it in a child like mine?
• Does this result change what we would do anyway?

A specialist may prescribe antibiotics when the result and the child’s clinical history point to SIBO.

In one placebo-controlled trial of children with long-term tummy pain, rifaximin, an antibiotic used for SIBO, did not improve symptoms more than placebo (Collins and Lin).

That trial doesn’t settle what helps a child with a clear medical reason for SIBO, which is a question for their specialist team.

Probiotics are often suggested too.

The ESPGHAN probiotic position paper found too little evidence to recommend for or against them in SIBO, so no specific probiotic can currently be recommended for it in children.

If a service recommends one, it’s fair to ask which strain they use and on what evidence.

A commercial IgG or microbiome report isn’t a reason to cut foods out of your child’s diet.

Removing a food needs a proper diagnosis, such as coeliac disease, or a clear clinical reason with supervision, and where appropriate, a plan to bring foods back.

When should I take my child to a doctor?

See your GP if your child’s tummy pain, bloating or constipation keeps coming back or doesn’t settle, or if you are worried.

Call NHS 111 or ask for an urgent GP appointment if your child develops a swollen tummy, has blood in their poo or wee, has constant pain for more than a day despite painkillers, or has a fever. The same applies if they are much thirstier or weeing much more or less than usual, their skin or eyes turn yellow, or they lose weight for no clear reason (Alder Hey). The NHS also advises calling 111 for diarrhoea lasting more than seven days or vomiting lasting more than two days.

Call 999 or go to A&E if your child becomes pale and floppy, drowsy or difficult to wake, vomits blood or green bile, develops severe pain despite painkillers, or, in boys, has pain in the testicles.

How the Happy Belly Club® can help

If your child has had the right medical checks and you are still trying to connect the stools, the pain, the food and the bad days on your own, the next step is someone reading the whole picture with you.

In the Happy Belly Club®, my 12-week one to one programme, I start with a full assessment. For example, I look at when the pain happens, what the poos are like and what you have already tried, then choose what to work on first. Then I change one thing at a time, in the right order, and we watch what your child’s gut does before the next step.

Frequently asked questions

About the author

Bahee Van de Bor

RD, BCAPSc PGDipDiet, Specialist Paediatric Dietitian

Bahee is a specialist paediatric dietitian based at Harley Street, with over 20 years of experience including 12 years at Great Ormond Street Hospital. She is lead author of the forthcoming UK dietetic guidance for IBS and functional abdominal pain in children, and presented at ESPGHAN 2026.

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