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Histamine Intolerance: Understanding Your Genetics and Managing Symptoms

Key takeaways:
~ Histamine intolerance is caused by an imbalance of too much histamine in the body that overwhelms your capacity to break it down.
~ The imbalance of histamine can be caused by your body producing too much histamine or by not being able to break down histamine from foods properly. Or both!
~ Genetic variants impact how well you break down histamine.
~ Understanding which variants you have can help you target the right diet and supplements to help with symptoms.

This article goes in-depth on the research into histamine intolerance, including the genetic variants that impact histamine levels. It concludes with diet,  lifestyle, and supplements solutions. Everything is fully referenced, so you can easily dig into the research yourself.

Want more on Histamine Intolerance? I wrote a whole book on what high histamine does in the body! Get your copy of Histamine Lifehacks here.

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Histamine intolerance: causes, symptoms, and treatment

Do you deal with sinus drainage after you eat? Periodic itching and hives? Migraines, irritability, anxiety, brain fog? The weird and seemingly unrelated symptoms of histamine intolerance can drive you nuts trying to figure out the root cause.

Classified as a biogenic amine, histamine is a molecule that plays many roles in the body.

Histamine’s many functions include:

  • causes allergic reactions,
  • acts within our immune defense system,
  • dilates blood vessels (vasodilatation)
  • acts as a neurotransmitter 
  • works as a signaling molecule in the stomach to release acid

While most of us think of histamine only during allergy season, histamine is a vital part of how your body works. The key is that you want the right amount – not too much!

What are the symptoms of histamine intolerance?

Histamine intolerance symptoms impact many different systems in the body, including[ref]:

  • Head: headaches & migraines
  • Mood: anxiety, irritability, brain fog
  • Stomach: acid reflux, nausea, stomach pain
  • Intestines: bloating, diarrhea, constipation
  • Heart: heart arrhythmia, dizziness
  • Sinuses: drainage, congestion
  • Skin: hives, weal, itching, flushing,
  • Sleep: insomnia, early waking

People with histamine intolerance usually have several of the symptoms above, but they likely won’t have all of the symptoms.[ref]

Historical note:
Too much histamine has been known for decades to cause scombroid poisoning – the type of food poisoning from eating fish that isn’t fresh.[ref]

Here’s a visual overview of what we are going to cover here:

Causes of histamine intolerance:

The two leading causes of histamine intolerance are:

  • not enough of the enzymes needed to break down histamine (DAO and HMNT)
    – and/or-
  • too much histamine being produced (gut microbes producing histamine, leaky gut, mast cells degranulating too easily, HDC variants, chronic exposure to allergens).

Clearing histamine from the body:

There are two ways your body breaks down and clears histamine: the DAO enzyme or the HMNT enzyme.[ref]

  1.  Diamine oxidase (DAO) enzyme: Histamine from foods or bacteria in your gut is broken down or metabolized using the DAO (diamine oxidase) enzyme. The DAO enzyme is produced in the villi lining the small intestines and is released to metabolize histamine.[ref]
  2. Histamine methyltransferase (HMNT) enzyme: The HMNT enzyme works throughout the body, including in the brain, to deactivate and break down histamine created by your cells.[ref]

Diamine Oxidase (DAO) enzyme:

Diamine oxidase is encoded by the AOC1 gene. It is mainly produced in the intestines to counteract histamine from foods and histamine created by intestinal bacteria. Foods containing a lot of histamines include aged cheeses, aged meats, fermented foods, and more.

Some species of bacteria in the gut, including those from some probiotics or fermented foods, can also increase histamine levels in the body.

People with histamine intolerance show altered gut microbiome composition as well as elevated levels of zonulin, which regulates tight junctions in the intestines. Excess zonulin causes ‘leaky gut’. [ref] A recent study of histamine intolerance patients found that they had “a significantly higher abundance of histamine-secreting bacteria…”[ref]

The DAO enzyme is also used by the body to break down other biogenic amines, including tyramine, putrescine, cadaverine, spermidine, and spermine. High levels of other biogenic amines can reduce the ability of DAO to break down histamine.[ref]

DAO degrades histamine into imidazole acetaldehyde, which is then quickly oxidized into imidazole acetic acid.[ref]

HMNT enzyme:

The HMNT enzyme breaks down histamine in the central nervous system.

Recent studies show exactly how important HNMT is in controlling brain histamine levels. Genetic variants that change HNMT levels in the brain are linked to an increased risk of neurodegenerative disorders such as Parkinson’s disease. Studies also link HNMT variants to an increased risk of migraines and ADHD.[ref] Rare mutations that inactivate the HNMT enzyme are linked to intellectual disability.[ref]

The HNMT enzyme acts throughout the body. Genetically decreased HNMT is also linked to atopic dermatitis or eczema.[ref] While DAO can also circulate in the periphery, HNMT is the only enzyme breaking down histamine as a neurotransmitter in the central nervous system.

When histamine is degraded with the help of the HNMT enzyme, it forms N-methylhistamine, which is unable to bind to histamine receptors. Note that a methyl group is needed in the reaction. The N-methylhistamine is further broken down with the MAO-B enzyme, forming N-methylimidazole acetaldehyde.[ref]

Creation of Histamine: The other side of the equation

Histamine is made from the amino acid histidine. It is an essential amino acid, meaning humans cannot make it in our bodies and must obtain it from diet. Histidine can be used in the body for several different purposes, including histamine production.

Histidine decarboxylase (HDC gene) is an enzyme that catalyzes the reaction of histidine into histamine. It does this inside various cell types, including creating histamine in large amounts in mast cells.

histidine -> histamine (PMC7463562)

Not enough histamine:
Without enough histidine decarboxylase (HDC), animal studies show behavior that resembles Tourette syndrome.

Genetic studies show that people with Tourette’s (vocal and motor tics) may have rare HDC gene mutations as a cause. The loss of histamine in the basal ganglia causes too much dopamine in that region of the brain, resulting in tics.[ref]

Too much histamine and the heart:
Histamine is also essential in the way that the heart muscle functions. Too much histamine here can be detrimental, and people with chronic heart failure have higher average plasma histamine levels. In fact, a genetic variant in the HDC gene that reduces histamine levels is linked to a significantly decreased risk of chronic heart failure.[ref]

Additionally, clinical trials show that blocking the H2 receptor is beneficial for chronic heart failure. Famotidine improved cardiac symptoms and ventricular remodeling. In the heart, histamine increases the force of contraction, and even as far back as 1913, histamine has been known to induce heart arrhythmias.[ref][ref]

Mast cells and histamine release:

Mast cells are a type of immune cell that creates and stores histamine. They are found in most tissues in the body, especially in areas of the body exposed to the outside world. Allergens cause mast cells to burst or degranulate and release histamine. Large numbers of mast cells are found in the skin, bronchial tree mucosa, and intestinal mucosa. In addition to allergens, viruses, bacteria, and fungi also activate mast cells.[ref]

The release of large amounts of histamine from mast cells can exacerbate problems with histamine from foods. Too many mast cells or mast cells that are two easily activated can lead to mast cell activation syndrome (MCAS).

Some researchers categorize histamine intolerance as a subset of mast cell activation syndrome (MCAS).

Related article: Mast cell activation syndrome – Genetics, causes, solutions

For more in-depth info on mast cells and histamine, check out Research Studies on Mast Cells and Histamine Intolerance, where I dive into all the different ways histamine can affect you.

Histamine receptors: understand the different effects of histamine

You may wonder why one molecule can cause so many different actions in the body…

How can histamine cause headaches and heartburn and hives? 

The function of histamine in a specific part of the body depends on the receptor it binds to.

Different histamine receptors are found in different parts of the body:[ref]

  • H1 receptors: Found in smooth muscle, endothelial cells (lining the blood vessels), the central nervous system, and mast cells. Activating the H1 receptors causes allergy-type symptoms such as itching, swelling, vasodilation, nose running, and skin reactions. H1 receptors are also important in asthma reactions.
  • H2 receptors: Acid is released when histamine activates the H2 receptors in the stomach. H2 receptors are also found in the intestinal tract and the walls of blood vessels. Mast cells also have H2 receptors, which, when activated, cause the release of more histamine. In the heart, H2 receptors are essential in controlling the rhythm.
  • H3 receptors: The central and peripheral nervous systems contain H3 receptors, which act as a feedback loop for histamine levels in the brain. Activating the H3 receptors impacts serotonin, norepinephrine, and acetylcholine release.[ref]
  • H4 receptors: These histamine receptors are at the core of the inflammatory response. H4 receptors are found in the bone marrow, basophils (a type of white blood cell), the thymus, small intestine, spleen, colon, and mast cells.[ref]


Gut impact: 
Three types of histamine receptors are found in the intestines: H1, H2, and H4. Interestingly, a study showed that people with food allergies and IBS had significantly higher levels of H1 and H2 receptors in their intestines.[ref] Histamine acts as a neurotransmitter in the gut and is involved in contractions of the intestinal muscles.[ref]

Histamine, Sleep, and Circadian Rhythm:

Histamine acts in the brain as a neurotransmitter. It is an alerting neurotransmitter, rising in the morning hours to wake us up. About 50% of the histamine in the brain is from mast cells.[ref]

Diphenhydramine, a commonly used antihistamine, has the side effect of making people sleepy. It is due to blocking the actions of histamine in the brain.

Altering histamine levels in the brain changes sleep:

  • In mice, eliminating the histamine receptors in the brain alters sleep patterns. Without histamine, mice were slower to wake up. They also had fragmented sleep and decreased non-REM sleep.[ref]
  • In another animal study, researchers decreased the number of mast cells in the brain, reducing histamine production. It did not affect the amount of time the mice slept overall, but it did affect their brain waves in sleep and their ability to bounce back after sleep deprivation.[ref]

In a recent study of people with suspected histamine intolerance, the researchers found that about 25% of the patients had a circadian change in histamine levels that differed from a control group. These patients had significantly reduced DAO enzyme levels and higher histamine levels during the day.[ref]


Histamine Intolerance Genotype Report:

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Lifehacks for histamine intolerance:

Below are the research-backed solutions for histamine intolerance. You may need to try several different ‘lifehacks’ to see which works best for you.

Low-histamine diet:

A low-histamine diet restricts foods with high levels of histamine or that cause the body to release histamine. To experiment with a low-histamine diet, eliminate all of the higher-histamine foods for a period of time to see how your body responds.

In general, foods that are fermented or aged are higher in histamine. High histamine foods include processed meats, cheeses (except farmer cheese), fish and seafood that isn’t completely fresh, spinach, chocolate, tomatoes, strawberries, wine, sake, and more.

High histamine foods list:

If you are considering a low histamine diet, I find this histamine food list to be the most thorough: Complete list of foods that are high in histamine (pdf)

Here are the highlights of what to avoid on a low-histamine diet:

  • Raw egg whites
  • Blue Cheese
  • Hard cheeses that are mature (e.g. cheddar, Colby)
  • Dried meat (jerky)
  • Cured ham
  • Most organ meats
  • Processed meats (salami, pepperoni, sausage, deli meat)
  • Smoked meat, BBQ
  • Anchovies
  • Fish that isn’t totally fresh
  • Meat that isn’t fresh, leftovers
  • Seafood (except ‘frozen at sea’)
  • Buckwheat, malted barley
  • Walnuts, pecans
  • Avocados
  • Eggplant
  • Hot peppers
  • Chickpeas
  • Lentils
  • Spinach
  • Soybeans, edamame
  • Tomatoes
  • Anything pickled
  • Bananas (when really ripe)
  • Citrus fruits
  • Chocolate
  • Guava
  • Kiwi
  • Pineapple
  • Strawberries
  • Nori, algae
  • Cumin
  • Mustard seeds
  • Soy sauce
  • Vinegar

You may find that some of these foods don’t cause histamine reactions, so it is a matter of trial and error to find out what works best for you.  For example, soy sauce causes histamine reactions in many people, but it may depend on which species of bacteria is used in the fermentation process. Certain bacteria can reduce the histamine content of soy sauce.[ref]

Note that alcohol can cause mast cells to release histamine. For some, this may cause flushing when drinking. But for people with histamine intolerance, even alcoholic drinks that are lower in histamine may still cause a reaction.[ref]

Related article: Alcohol, mast cells, and histamine

What does a low-histamine diet do?

  • Decreasing the amount of histamine you take into your body will lower the overall amount of histamine circulating in your body.
  • Research studies show that a low histamine diet helps with chronic urticaria (itchiness, hives), migraines, stomach problems, and asthma.[ref][ref]

Should you maintain a low histamine diet long-term?

Trying a low-histamine diet for a period of time can give you a lot of insight into how histamine affects your body, but it may not be a diet you want to continue long-term. A low-histamine diet restricts many healthy foods that you may enjoy, such as spinach, strawberries, and avocados.

Use a low histamine diet as a tool to learn which histamine-containing foods bother you the most. It can also be a short-term way of getting histamine responses under control.

Low FODMAPs diet: histamine and gut problems

Interestingly, a randomized controlled study for people diagnosed with IBS found that a low FODMAPs diet reduced symptoms and reduced histamine levels.

It could mean that a FODMAPs diet works because IBS is related to histamine intolerance – or – it could mean that the people diagnosed with IBS were really dealing with gut-related histamine symptoms.[ref] Additionally, the low FODMAPs diet may help to decrease intestinal barrier permeability.

A low FODMAPs diet cuts out a lot of high histamine foods, so it could reduce histamine levels by eating fewer foods high in histamine. On the other hand, a low FODMAPs diet impacts the gut microbiome and histamine-producing bacteria. Animal studies also link IBS to mast cell activation in the colon, so changing the gut microbiome with a FODMAPs diet may also impact colonic mast cells.[ref]

Learn more about what is included in a low FODMAPs diet: Starting a Low FODMAPs diet

Research on supplements for Histamine Intolerance:

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Related Articles and Topics:

Mast cells: MCAS, genetics, and solutions
Mast Cell Activation Syndrome, or MCAS, is a recently recognized disease involving mast cells that misbehave in various ways. Symptoms of MCAS can include abdominal pain, nausea, itching, flushing, hives, headaches, heart palpitations, anxiety, brain fog, and anaphylaxis. Dive into the research into mast cells, genetics, and solutions.

Notes about Histamine and Mast Cells
A compilation of notes and reference studies on the functioning of mast cells and histamine receptors.

Tyramine: The Cheese Effect and Your Genes
Tyramine is another biogenic amine found in a lot of the same foods as histamine. An inability to break down tyramine can cause a variety of symptoms.

Recipes and Foods for Histamine Intolerance
Interested in low histamine foods and recipes? This article focuses on foods high in histamine so you can easily eliminate them from your diet.

Nickel allergy:
Systemic symptoms such as gastrointestinal issues or fatigue can be caused by eating foods higher in nickel.


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Originally published April, 2015. 


About the Author:
Debbie Moon is the founder of Genetic Lifehacks. Fascinated by the connections between genes, diet, and health, her goal is to help you understand how to apply genetics to your diet and lifestyle decisions. Debbie has a BS in engineering from Colorado School of Mines and an MSc in biological sciences from Clemson University. Debbie combines an engineering mindset with a biological systems approach to help you understand how genetic differences impact your optimal health.