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Why You Should Consider Gut Health Testing for Histamine Intolerance

Updated: Feb 17

There are a number of different factors that can contribute to histamine intolerance, and gut imbalances are among the most significant.

I have determined that testing for gut health imbalances can be helpful in order to identify specific imbalances that may be underlying your histamine intolerance, and in order to personalize diet and lifestyle recommendations to your individual case.

Testing for Histamine Intolerance

One of the most common questions I hear about histamine intolerance is whether or not it can be tested for. There are a few different kinds of tests on the market for histamine intolerance, but the utility of many of these tests is questionable, and there is no definitive test that will diagnose the condition.

The best “test” to determine whether or not you have dietary histamine intolerance is generally thought to be to follow a low histamine diet for four weeks. Symptoms are observed during the elimination period and, as a trial, when reintroducing histamine.

If symptoms improve on a low histamine diet and return when histamine is reintroduced, and if other diagnoses have been ruled out, you may be diagnosed with histamine intolerance.

That said, there are a few other kinds of tests that might be helpful in the management of histamine intolerance, including those that look at gut imbalances.

The Links Between Histamine Intolerance and Gut Health

There are several important connections between histamine and the gut, and addressing gut health is essential when it comes to treating histamine intolerance.

It is common for people with histamine intolerance to also experience gastrointestinal symptoms, as explained in this article. In particular, irritable bowel syndrome (IBS) and histamine intolerance are highly correlated (1).

Imbalances in the gut can also lead to a number of different kinds of symptoms throughout the body, and gut health issues may be connected to histamine intolerance even if digestive symptoms are not present.

The links between histamine intolerance and the gut include:

  • Gut dysbiosis can lead to less DAO production or activity. The enzyme diamine oxidase (DAO), which is responsible for breaking down dietary histamine, is mostly produced in the gut. If gut health is poor, less DAO is produced, and histamine may build up in excess (2). This is supported by the fact that research has shown a correlation between lower DAO levels, excess histamine, and gastrointestinal conditions such as Crohn’s disease and ulcerative colitis (3).

  • Certain strains of gut bacteria produce histamine. Certain strains of bacteria produce histamine, so when there is an overgrowth of those strains of bacteria in the digestive tract, histamine levels may rise beyond what is typical. Small Intestinal Bacterial Overgrowth (SIBO) can occur in tandem with histamine intolerance (4).

  • Dysbiosis can lead to immune system dysfunction and increased mast cell activation. There is a link between gut dysbiosis and histamine production (5). Dysbiosis, or an imbalance of bacteria, can contribute to increased intestinal permeability (leaky gut) and trigger an inflammatory immune response. This includes the activation of mast cells, a type of immune cell that releases histamine. When the inflammatory immune response is chronic, mast cells may be overactivated, leading to a rise in histamine levels.

Gut Health Testing for Histamine Intolerance

Given the multiple connections described above, it makes sense to evaluate gut health in the process of determining the underlying causes behind your histamine intolerance.

There are a few different kinds of tests that may be helpful, and a functional medicine practitioner can help you to determine which one(s) to start with.

Gut Microbiome Testing

There are a number of DNA-based stool tests that are designed to analyze the makeup of your gut microbiome and identify bacterial imbalances. One such test is the GI-MAP, which is commonly recommended for individuals with symptoms of IBS/IBD, SIBO, intestinal permeability (leaky gut), and autoimmune conditions.

The GI-MAP test results reveal the genetic makeup of the select gut organisms, including both beneficial and pathogenic bacteria. This information can be used to understand whether histamine-producing strains of bacteria may be overabundant in the gut.

The test also looks at markers of inflammation and immune function, given that the majority of the body’s immune system is based in the gut. These markers can shed light on whether there is overactivation of the immune system, which may be leading to excess histamine.

SIBO Breath Testing

Given the connection between small intestinal bacterial overgrowth (SIBO) and histamine production, testing for SIBO can be very helpful in getting to the root of your histamine intolerance.

A few breath tests are available to identify SIBO, at which point a practitioner can guide you through a treatment plan in order to reduce the overgrown bacteria and restore balance in the gut.

Zonulin Testing

Zonulin, a marker of intestinal permeability (leaky gut), is another useful testing option. Leaky gut is associated with increased inflammation, immune system dysfunction, and mast cell activation.

A functional medicine practitioner can check for elevated zonulin levels with a simple blood test, or add it to the GIMAP.

Next Steps

In conclusion, if you are experiencing symptoms of histamine intolerance, I often recommend gut health testing as an important step toward understanding the basis for your condition.

1. Working with a healthcare practitioner knowledgeable in MCAS and histamine intolerance is the best way to get to the root cause of your symptoms and to create an individualized treatment plan. I welcome you to start a personalized functional medicine consultation with me. You may book your consultation here.

2. Check out my Histamine Intolerance Course here. Learn on your own time, from anywhere. Get an inside look at the most helpful functional medicine tests for pinpointing imbalances, ways to identify and manage the most common (and sometimes surprising) mast cell triggers, and learn what to eat, what to avoid, and why.


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