What Do Hydrogen Breath Tests Diagnose?

Doctors use hydrogen breath tests to diagnose a few different gastrointestinal conditions. At Healthpath, we use a breath test that measures both hydrogen and methane to find out if you have SIBO (small intestinal bacterial overgrowth).

Could taking a hydrogen breath test help you solve your health puzzle?

What does a breath test diagnose?

There are many different kinds of breath tests, used to diagnose or investigate many different conditions. The most common are:

  • H. pylori
  • SIBO
  • Lactose intolerance
  • Fructose intolerance

Out of these, H. pylori is the only one that doesn’t measure hydrogen levels in the breath. Interestingly, researchers are currently looking at how breath testing could help us to diagnose and treat the following conditions:

The three main conditions that hydrogen breath tests diagnose are SIBO, lactose intolerance and fructose intolerance.


A SIBO test shows the levels of hydrogen present in your small intestine by measuring the number of particles in your breath. It might seem strange that we measure gases in your gut by looking at the levels in your breath, but while 80% of this gas remains in your intestines, the other 20% is absorbed into your blood and travels round to your lungs—where you breathe it out [Source: PubMed].

Because your body doesn’t produce hydrogen on its own, we know that any hydrogen that shows up on a SIBO test is produced by bacteria. High levels of hydrogen is a diagnostic sign of an overgrowth of bacteria in your small intestine.

A good SIBO test will also measure the levels of methane in your breath. Methane isn’t produced by bacteria, but from microbes known as ‘archaea’. High levels of methane on a breath test indicate an overgrowth of archaea in your small intestine, but most experts still call it SIBO anyway, to avoid confusion.

You can check out our SIBO test, along with all our other tests, on our tests page.

Could your symptoms be SIBO?

View our at home SIBO test

Lactose intolerance

Lactose malabsorption is a common condition caused by a lack of the enzyme that helps you to digest it—lactase—in your small intestine. If you have lactose intolerance, most dairy products will give you symptoms like nausea, bloating, and pain.

Foods highest in lactose, which you should avoid if you have lactose intolerance, include:

  • Milk
  • Cream
  • Soft cheeses

However not all dairy products contain significant amounts of lactose. These only contain trace amounts:

  • Aged cheese (like parmesan)
  • Butter
  • Ghee

As a baby, you have a lot of lactase, but levels drop when you start eating solid food. A lot depends on your ethnicity: if your ancestors drank milk, you probably inherited the ability to digest it into adulthood. The highest rates of lactose malabsorption are in Asian populations, Native Americans and Africans (60-100 percent), while 2-22 percent of Northern Europeans have lactose intolerance.

SIBO can also cause lactose intolerance. If you have SIBO, treating it could help you to digest dairy products. However, there are other reasons why you might have problems digesting dairy, like dysbiosis in your large intestine [Source: PubMed], or an immune reaction [Source: PubMed].

Fructose intolerance

There are different kinds of fructose intolerance. Hereditary fructose intolerance is a rare genetic disorder. Most people are not born with it, but develop it later in life.

If you don’t absorb fructose (a type of sugar found mostly in fruit) properly in your small intestine, you can get symptoms like bloating, diarrhoea and flatulence. 

Fructose is a type of ‘FODMAP’, so a low-FODMAP diet is low in fructose and other types of carbohydrates that have been found to cause IBS symptoms. You can find out more about the low-FODMAP diet in our blog NHS FODMAP diet: the complete guide.

For many people this can provide some symptom relief in the short term, but we don’t recommend that you follow it for more than six weeks, because it doesn’t tackle the root cause of your symptoms.

The very foods that are high in FODMAPs are the foods that contain the prebiotic fibres that fuel your good gut bacteria. 

As with lactose malabsorption, fructose malabsorption is often a consequence of SIBO. You may find that tackling SIBO allows you to tolerate the fruits and vegetables that you’re currently having to avoid.

What does a positive hydrogen breath test mean?

A positive hydrogen breath test means that you have too many hydrogen-producing bacteria in your gut.

Because hydrogen breath tests are used to diagnose a few different conditions, there’s no universal level that defines a positive or negative result: it depends on the particular test you take.

At Healthpath, the only hydrogen breath test we use is for SIBO, which also measures methane levels. For our SIBO test, you have a positive hydrogen result if you have over 20 ppm (parts per million) before 90 minutes into the test. To find out what happens during a SIBO test, read our blog SIBO test: all your questions answered.

How long does it take to get results from a hydrogen breath test?

We’ll post your results on your online account a maximum of one week after we receive your breath samples. If you get a SIBO test from us, you’ll get a diet plan, supplement protocol and professional advice tailored to you from a Registered Nutritional Therapist included in the price.

There are many other UK companies that provide at-home SIBO testing now, but as far as we know, their tests don’t come with bespoke plans or advice. Most of them will tell you how long you’ll wait for your results on their website.

Test, don't guess. Shop our hydrogen methane test.

View our at home SIBO test

Are hydrogen breath tests accurate?

Very few tests are perfect. Some experts question the accuracy of hydrogen breath tests, for a few reasons:

Not all bacteria produce hydrogen

The hydrogen breath test depends on the presence of hydrogen producing bacteria. However some people may have an overgrowth of non‐hydrogen producing bacteria, which can yield false negative results [Source: PubMed]. However, some studies disprove this claim [Source: PubMed].

A SIBO test should measure both hydrogen and methane, as some microbes (known as archaea) produce methane. A test that only measures hydrogen is more likely to produce a false negative result.

False positive results

Carbohydrate malabsorption in chronic pancreatitis and coeliac disease may result in a false positive test for SIBO [Source: PubMed] due to rapid transit (food moving too quickly through the digestive system). False positive results may also be due to the bacteria in your mouth, or if you haven’t followed the correct low-fibre diet the day before the test.

False negative results

According to this study [Source: PubMed] ‘delayed gastric emptying’ (when there’s a problem with your stomach releasing its contents into the small intestine) may cause false negative test results owing to food moving too slowly through the gut.

Despite the above limitations, most experts agree that hydrogen breath tests are simple and safe, ‘providing us with an easy tool to unravel symptoms that are often difficult to explain [Source: PubMed].’

The North American Consensus (a meeting of 17 clinicians and scientists to define industry standards for breath testing for SIBO and carbohydrate malabsorption) concluded that breath testing ‘is a useful, inexpensive, simple and safe diagnostic test in the evaluation of common gastroenterology problems [Source: PubMed].’

Key takeaways

  • Hydrogen breath tests are commonly used to diagnose malabsorption of carbohydrates like lactose and fructose, and SIBO (small intestinal bacterial overgrowth).
  • Carbohydrate malabsorption is a common symptom of SIBO, but not all carbohydrate malabsorption is down to SIBO.
  • A good SIBO test measures both hydrogen and methane levels.
  • Both lactose and fructose are FODMAPs, so a low-FODMAP diet may reduce your symptoms if you have lactose intolerance, fructose intolerance and/or SIBO.
  • While a low-FODMAP diet may make you more comfortable in the short term, it doesn’t address the root cause of your symptoms: too many hydrogen-producing bacteria in your gut.
  • While the SIBO test isn’t perfect, experts agree it’s an invaluable tool in working out why some patients have persistent digestive symptoms.


Alexandra Falconer MA (Dist) DipCNM mBANT is a Registered Nutritional Therapist specialising in IBS and related conditions. A graduate of Brighton’s College of Naturopathic Medicine, she is committed to fighting the root causes of chronic illness and bringing functional medicine to everyone who needs it.

Before her natural health career, Alex was a journalist and copywriter. She continues to write for magazines and media agencies, and now combines her two great passions—writing and health—by creating content that empowers people to claim their right to a healthy body and mind.



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