Most people associate histamine with seasonal allergies like runny noses, itchy eyes, and skin rashes. But this powerful molecule plays a much larger role in the body. Histamine is also involved in brain function, gastric acid secretion, immune signalling, and reproductive health.
For some, however, histamine becomes a problem because the body can’t break it down properly and it begins to accumulate and cause uncomfortable, sometimes debilitating, symptoms.
What Is Histamine Intolerance (HIT)?
Histamine intolerance occurs when there’s too much histamine in the body and not enough capacity to break it down. This isn’t an allergy to histamine, it’s a processing problem.
To break histamine down, there are two primary enzymes involved:
- Diamine oxidase (DAO): DAO degrades dietary histamine in the gut. If DAO is deficient or inactive then dietary histamine builds up and causes issues.
- Histamine-N-methyltransferase (HNMT): HNMT handles histamine breakdown inside cells within other tissues such as the brain, ovaries, kidneys, liver and respiratory system. HNMT depends on methylation to function, so individuals with MTHFR polymorphisms may struggle with histamine overload.
What are the symptoms of HIT?
Symptoms can include:
- Digestive issues (bloating, nausea, diarrhoea)
- Headaches and migraines
- Skin rashes or hives, itching, redness
- Nasal congestion, sneezing, runny nose
- Anxiety, irritability
- Insomnia
- Vertigo
- Heart palpitations
Plus cyclical hormone-related symptoms in women:
- Painful periods
- Heavy periods
- Pain around ovulation
- PMS or PMDD symptoms
- Cyclical headaches or migraines
- Tender or swollen breasts pre-menstrually
- Endometriosis flares
What causes histamine intolerance (HIT)?
Generally, in HIT there is an inability to break down histamine properly. But the reasons for why there is impaired breakdown need to be examined in order to treat effectively.
1. Deficiency of the required enzyme
Impaired breakdown of histamine could be due to deficiency or dysfunction with the DAO or HNMT enzyme.
Low DAO (or impaired DAO function):
This could be due to:
- Gut inflammation (IBS, coeliac disease, ulcerative colitis, Crohn’s disease)
- Intestinal dysbiosis (imbalanced gut flora)
- Gastrointestinal infections
- Alcohol (inhibits DAO activity)
- Certain medications (e.g. NSAIDs, antibiotics, antidepressants, antihypertensives)
- Genetic polymorphisms in the DAO gene
- Nutrient deficiencies (vitamin B6, vitamin C, copper, zinc)
Low HNMT (or impaired HNMT function):
Can be due to:
- MTHFR gene polymorphisms (this affects methylation)
- Low SAMe (S-adenosylmethionine) levels
- Deficiencies in folate, B12, B6
- Elevated homocysteine (indicates methylation issues)
2. Gut Dysbiosis and Inflammation
Improving gut health is paramount to managing histamine intolerance. Most of our DAO is produced within the gut. Aspects such as mucosal integrity and microflora composition determine how well the gut performs its functions.
- Some gut bacteria can produce histamine, worsening the histamine load
- Dysbiosis reduces DAO production and damages the gut lining (“leaky gut”), impairing histamine clearance
- Conditions like SIBO (Small Intestinal Bacterial Overgrowth) are common HIT contributors
3. Hormonal Influences
One of histamine’s influential roles is in the reproductive system. Oestradiol (a form of oestrogen) can trigger histamine release in the uterus and ovaries, and histamine can stimulate greater oestrogen production in return. This can create a vicious cycle.
Whilst some histamine is needed for ovulation and fertility, too much can wreak havoc. That is when symptoms like painful or heavy periods, menstrual migraines and irregular cycles can occur.
HIT symptoms often worsen around ovulation or menstruation due to the rise in oestrogen and subsequent increase in histamine. Puberty and perimenopause are common times for histamine intolerance symptoms to manifest due to the fluctuating oestrogen levels.
4. Genetic Factors
- DAO gene polymorphisms reduce DAO enzyme activity
- MTHFR polymorphisms impair methylation, affecting HNMT function
5. Nutrient Deficiencies
Histamine breakdown requires several cofactors:
- Vitamin B6 – cofactor for DAO production
- Vitamin C – Stabilises DAO and reduces histamine
- Zinc – inhibits histamine release
- Copper – DAO cofactor
- Folate and B12 – Nutrients required for methylation (HNMT function)
- Magnesium – DAO cofactor
- Iron – DAO cofactor
Deficiencies in any of these nutrients can play a role in histamine intolerance symptoms.
What role does diet play in HIT?
Some foods naturally contain high amounts of histamine and some foods trigger histamine release. In a healthy person, this isn’t a problem, but in someone with impaired clearance, histamine builds up quickly and causes problems.
Following a low-histamine diet can be beneficial to reduce symptoms whilst other aspects are worked on, such as gut health and hormone balancing. After a period of time, foods can be reintroduced slowly, whilst the person assesses if their tolerance for each food has improved.
High-histamine foods include:
- Fermented foods (sauerkraut, kimchi, yogurt)
- Aged cheese
- Processed or smoked meats
- Vinegar
- Leftovers (histamine levels rise as food sits)
- Shellfish
- Spinach, tomatoes, eggplant, avocado
- Alcohol, especially wine (both a trigger and DAO inhibitor)
Testing options
Functional testing can be helpful for determining whether histamine is playing a role in causing symptoms and for guiding treatment direction. Useful tests include:
- Whole Blood Histamine
- Elevated levels can suggest histamine overload
- Best measured after fasting and with no antihistamines for 5+ days
- Methylation Profile
- Homocysteine, B12, folate, SAMe, and MTHFR genetic polymorphisms
- Useful if HNMT function or methylation pathway is suspected to be impaired
- Organic Acids Test (OAT)
- Assesses gut dysbiosis, mould, yeast, and nutrient cofactors for methylation
- Stool Testing / GI Mapping
- Looks at gut flora balance, inflammation, pathogens, and mucosal health
- Can identify dysbiosis impairing DAO production
Naturopathic Treatment Approaches
Dietary Support
- Low-histamine diet: Initially, this can be helpful to alleviate symptoms, in conjunction with other treatment measures. Eventually, foods are reintroduced slowly.
- In particular, avoid: fermented foods, alcohol, smoked meats, leftovers, vinegars, aged cheeses.
Supplementation
Key goals are to provide necessary nutrients to produce DAO (like vitamin B6, copper, iron, magnesium and vitamin C) and to stabilise mast cells and inhibit excessive histamine release (quercetin and zinc are important here).
For patients with MTHFR polymorphisms, nutrients required for methylation may need to be supplied as well as implementing specific dietary practices.
Overall gut healing and microbiome work is necessary too. The specific approach differs based on what is revealed through GI stool mapping. Throwing probiotics at a dysbiotic gut is not always helpful as some strains can produce histamine and worsen symptoms. A tailored, careful approach is required.
Stress management
Stress impact can never be overlooked. Chronic stress triggers ongoing histamine release.
Measures such as mindfulness, sleep hygiene, gentle exercise along with herbal medicine and nutrients that nourish and support the nervous system can help calm down the stress response and its impact on histamine release.
Final thoughts – Histamine intolerance and its resulting symptoms can be frustrating and overwhelming to contend with. Naturopathic medicine offers a comprehensive and compassionate approach. By combining advanced testing with root-cause thinking, a naturopath can help you identify triggers, support natural healing pathways, and move toward symptom relief and resilience.
This article is for educational purposes only and is not intended to replace professional medical advice. Always consult with your healthcare provider before making changes to your treatment plan.