SIBO and Histamine Intolerance: Symptoms, Testing and Diet

In short: histamine intolerance is a poorly defined condition in which histamine from food is not broken down properly in the gut, mainly because of low activity of the enzyme diamine oxidaseDiamine oxidase (DAO) An enzyme made by the cells lining the small intestine that breaks down histamine from food. When the lining is damaged, low DAO activity can cause histamine intolerance. (DAO)¹. Its symptoms, especially bloating, overlap heavily with SIBO². A link between the two is plausible: some gut bacteria make histamine, and damage to the gut lining lowers DAO¹⁴. However, no study has tested whether SIBO causes histamine intolerance or whether treating SIBO improves it. There is no validated test for histamine intolerance, and the main approach is a low-histamine diet followed by reintroduction⁸.

What histamine intolerance is

Histamine is a natural chemical that the body uses in allergic reactions, stomach acid production and nerve signaling. It is also found in many foods, especially fermented ones¹. Normally, DAO made in the gut breaks down histamine from food before much of it is absorbed. When DAO activity is low, histamine can build up and cause symptoms¹³.

Low DAO can have several causes¹:

• Genetics. Some people inherit variants that lower DAO activity.
• Gut diseases that damage the lining. In inflammatory bowel disease, the loss of DAO activity tracks the severity of damage to the gut lining.
• Alcohol, other food amines and medicines. These can block DAO temporarily. An estimated 20% of Europeans regularly take a medicine that inhibits DAO.

Histamine intolerance is not an allergy: it is a food intolerance, which does not involve the immune system⁷.

Symptoms and the overlap with SIBO

Symptoms of histamine intolerance are varied and nonspecific, and they can appear outside the gut as well as in it³. In a 2019 survey of 62 people with suspected histamine intolerance and low blood DAO, bloating was both the most common and the most severe symptom, followed by fullness after meals, diarrhea, abdominal pain and constipation. The 62 people reported 276 different combinations of just two symptoms².

Bloating, diarrhea and abdominal pain are also the core symptoms of SIBO, which is one reason the two are easily confused.

Is there a link with SIBO?

There are two plausible mechanisms, but neither has been tested in people with SIBO.

Histamine-making bacteria. Many bacteria can produce histamine. In spoiled fish, some of the most prolific histamine formers, such as Klebsiella pneumoniae and Morganella morganii, belong to the Enterobacteriaceae family¹, a group that also lives in the gut. In a 2022 study, people with histamine intolerance had more histamine-secreting bacteria in their stool than healthy people, including Proteus, Staphylococcus and several Enterobacteriaceae, and fewer bacteria linked to gut health⁴. A follow-up pilot study of just 5 women found that 9 months of a low-histamine diet with DAO supplements reduced some of these bacteria⁵. Both studies examined stool, which reflects the colon rather than the small intestine.

Damage to the gut lining. DAO is made mainly by the cells lining the intestine, and diseases that damage this lining reduce DAO activity¹³. SIBO has been linked to changes in the small-intestinal lining (see SIBO and leaky gut), so it could in principle lower DAO, but we found no study that has measured this.

The only SIBO study we found that measured histamine was a 2024 open-label trial of herbal supplements in 16 people with SIBO. After 10 weeks, there was no significant change in blood DAO, histamine or the ratio between them⁶. The study was small and had no control group.

How histamine intolerance is diagnosed

There is no validated test⁸. Diagnosis is mainly clinical: a doctor rules out conditions with similar symptoms, such as food allergy, celiac disease, IBS and SIBO, and then looks at whether symptoms improve on a low-histamine diet⁷.

• Blood DAO tests are available, but blood DAO levels have not been shown to reflect DAO activity in the gut³. Studies of people with histamine intolerance have found low blood DAO in anywhere from 24% to 71% of patients¹.
• A histamine challenge (swallowing histamine or a placebo without knowing which) has been proposed, but it carries a risk of severe reactions, and one multicentre study found its results were not reproducible in the same person¹.
• A SIBO breath test can be done separately if your symptoms fit SIBO; see breath tests explained.

Low-histamine diet

A low-histamine diet is considered the main treatment, and a good response to it is often taken as confirmation of the diagnosis⁷. There is no single standard version: the foods excluded differ between published diets¹. Fermented foods are excluded in almost all of them, along with spinach, eggplant and tomatoes. Fresh meat and fish are generally allowed, because histamine builds up as they age¹.

This creates some tension with SIBO advice. Fermented foods such as sauerkraut and kefir are often suggested for gut health but are high in histamine. If you are on a SIBO diet as well, the combined restrictions can become narrow; a dietitian can help keep it balanced. Like other elimination diets, a low-histamine diet is meant to be followed by gradual reintroduction to find your own threshold⁸. See reintroducing foods after SIBO.

DAO supplements

DAO supplements are taken before meals to help break down histamine in food. Two small randomized trials have tested them, both in people with low blood DAO:

• In a 2019 double-blind trial of 100 people with migraine, a month of DAO shortened migraine attacks from 6.1 to 4.8 hours on average. Attacks also shortened on placebo (7.5 to 6.7 hours), so the difference between DAO and placebo was not statistically significant. The number of attacks and pain intensity improved similarly in both groups⁹.
• In a 2018 double-blind crossover trial of 22 people with chronic hives, 30 days of DAO reduced hive scores in those with low DAO, and they could slightly reduce their antihistamine dose¹⁰.

Neither trial was in people with SIBO or with digestive symptoms as the main problem. A 2025 review concluded that the clinical evidence for DAO is limited but suggests some benefit; that review was funded by a company that makes a DAO ingredient⁸. When antihistamine medicines are used, a 2021 review recommends newer (second- or third-generation) antihistamines for a limited time⁷.

Common questions

Can SIBO cause histamine intolerance?

It is possible but unproven. Some histamine-producing bacteria are the kind that can overgrow, and gut damage lowers DAO¹⁴, but no study has tested this in people with SIBO.

Will treating SIBO fix histamine intolerance?

We found no study that has tested this. In one small herbal treatment study, blood DAO and histamine did not change⁶.

Are probiotics and fermented foods safe with histamine intolerance?

Fermented foods are excluded on nearly every low-histamine diet¹. Some lactic acid bacteria, the group many probiotics come from, can produce histamine¹; see our probiotics guide for what is known about probiotics in SIBO.