Struggling with unexplained headaches, gut issues, or allergic-type reactions that don’t seem to have a clear cause? Histamine intolerance is often the hidden driver, but when it comes to histamine intolerance testing, the process can be surprisingly tricky.
In my clinical practice at Byron Herbalist, I see histamine-related symptoms every week, and one thing is clear: there’s no single, perfect test to diagnose it. That’s why I focus on a targeted approach that combines clinical experience, the latest research, and smart functional testing strategies.
In this guide, I’ll walk you through the best ways to approach histamine intolerance testing, what works, what doesn’t, and how you can get to the root cause of your symptoms naturally.
What Is Histamine Intolerance? Common Symptoms to Know
Most of you reading this will already know that histamine intolerance is an issue. Many may be surprised at the broad and often debilitating symptoms that histamine overload can cause.
The most common symptoms I’ve seen in the Byron Herbalist clinic would be
Below is a great diagram connecting histamine to the various histamine receptors in the body and their impact the body (think symptoms)
Image take from: Histamine and Histamine Intolerance
Why Histamine Intolerance Is Hard to Test
The most important thing to cover here, and I wish it wasn’t the case, is that there is no great direct test for histamine intolerance. This is probably why so many people go for so long with this condition and can’t find the answers they need to get better!
We have two blood tests that are commonly recommended in the literature. Both blood histamine and DAO are notoriously inaccurate. Blood histamine being high would be an indicator of histamine overload and low DAO, which is the main enzyme that detoxifies histamine outside of the cell called diamine oxidase.
I never recommend these labs. They can be quite expensive here in Australia and I find them a waste of money at best and misleading at worst for most of my patients. If you have these labs and they are showing high histamine and/or low DAO that helps, and if these labs were free and easy to access I would order them on every patient where histamine intolerance is suspected but, at least here in Australia that isn’t the case.
(Serum DAO’s) ‘capability to discriminate between patients with a high probability of HIT (histamine intolerance) and those with a low probability of HIT is limited. Consequently, relying solely on DAO determination without appropriate clinical evaluation is not suitable for diagnosing HIT. Nonetheless, DAO determination can serve as a valuable additional tool to support clinically based diagnosis. It is essential to emphasise that the current diagnosis of HIT primarily relies on clinical evaluation, and the integration of DAO determination with clinical assessment can offer a more comprehensive approach to diagnosing HIT’
The other approach that is commonly recommended for allergy testing which I am a fan of would be testing for blood IgE levels with your doctor – I have seen these THROUGH the roof with some very symptomatic patients – and even allergen specific IgE blood testing where they can review what you may be reacting to in the environment – could be mould, could be pollen or grasses and another big one would be dust mites too.
Now this won’t confirm histamine intolerance directly but the connection between
There is a great decision making tree below from a very helpful paper published in the journal Nutrients called Histamine Intolerance—The More We Know the Less We Know. A Review. Here they look to rule in or out IgE mediated histamine reactions almost immediately in the histamine intolerance treatment plan.
Image above from: Histamine Intolerance—The More We Know the Less We Know. A Review
Finally the classic skin prick allergy test, again ordered by your doctor, can be helpful to assess the level of your sensitivities.
The Best Tests for Histamine Intolerance
The hardest part with histamine intolerance is to find the root cause driver. It’s a minefield and can be like peeling back an onion with some patients. I’ve spent years working on this very issue and am in the process of writing either an ebook or a short course that will help you walk through this process.
Jump on the waitlist below and I’ll let you know when it’s ready!
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First and foremost the best way to determine whether histamine is driving your symptoms is to go on a low histamine diet. If you feel significantly better, i.e. if your symptoms improve dramatically over 4-8 weeks on a low histamine diet then we can be pretty sure that histamine is driving your symptoms.
Determining histamine is a driver is only half of the battle. You’ve gone on a low histamine diet, you feel better, now what?
I have found, and this is a little foreshadowing of the e-book/course which goes in depth on this front, is that the vast majority of histamine intolerance can stem from the following.
You may have one of these issues, a few or in the most severe cases all of them.
- Microbiome imbalances
- Mast cell issues
- Nutrient deficiencies
- Genetics
The common labs that I would run to determine each of these, and remember I would NEVER run all of them unless someone was just so incredibly unwell or cashed up and wanted to spend the money out of interest would be the following
Microbiome imbalances driving histamine intolerance
An advanced stool test or a SIBO breath test or both. Look for a DNA based stool test that will also report on leaky gut, inflammation, enzyme production markers and more as well as bacterial, fungal and parasitic infections and overgrowths.
Microbes like Klebsiella which can be particularly tricky to treat in certain cases and even fungal overgrowths are well known drivers of histamine intolerance. SIBO is a third big driver of gut damage leading to histamine overgrowth and can be a complete minefield to approach. For more info check out our Complete Guide To Small Intestinal Bacterial Overgrowth here.
Here in Australia I like and recommend the Complete Microbiome Mapping stool test and I also really like the GI-effects by genova diagnostics which should be available in most countries.
New to the scene is Co-biome from Microba, again Australia only. This is a bit pricier but combines the best from all stool tests and gives you the most in depth view if needed.
SIBO breath testing can be another minefield and instead of reviewing that approach I’ll just link to the video here and you can check it out when you have time.
Image above showing the Complete Microbiome Mapping stool test from Nutripath.
Mast cell issues driving histamine intolerance
Getting to the bottom of whether mast cells are involved is quite difficult. If I am almost convinced there is a mast cell activation issue at play I will refer my patients back to their doctor. Frequently they then get referred onto an immunologist who will run very specialised testing to determine whether the mast cells are activated and degranulating excessively.
The most important test from my clinical perspective is an OAT test from Mosaic labs (formerly great plains labs) which will look for many many different mast cell triggers including bacterial and fungal – mould growing in the gut is a major driver here – indicators of mould exposure in the environment but not directly = here you’ll need to run a mycotoxin urine test as well – and heavy metal indicators – again not directly but it will give you an idea and you can run a HMA if needed.
Image above showing an Organic Acid Test from Mosaic labs
Nutrient deficiencies driving histamine intolerance
The 3rd root cause driver of histamine intolerance is possible nutrient deficiencies. Here I will refer to the incredible work of Ben Lynch and his fantastically helpful pathway planners. I live in these pathway planners, I’ll form a suspicion, do some testing and then use the lab results and these pathway planners to walk patients through the cause and effect of nutrient deficiencies on their body and symptoms of histamine intolerance.
Image above showing the pathway planners from Seeking Health.
Again the OAT test is a great place to start.
Other nutrients here that can be tested for with a simple blood test would be zinc.
More advanced nutrient testing which I will rarely run would be the SAM:SAH ratio and a patient’s ability to methylate directly. Again if these tests were free or money grew on trees I would order it every time but there are better places to spend your money most of the time!
Genetics driving histamine intolerance
Finally the last strong driver of histamine intolerance is your individual genetics.
There is a huge amount of buzz around methylation at the moment (and for the past 5-10 years too) specifically around the MTHFR gene which codes for the enzyme that converts folate (specifically 5,10 methylene tetrahydrofolate) into methylated B9 or 5-methyltetrahydrofolate. This spins off into the methylation cycle which works to convert homocysteine into SAMe (s adenosylmethionine) which is the universal methyl donor and works to power over 200 different enzymes in the body.
Simply put it is damn important we make this in sufficient amounts!
Now back to genetics, if you have an MTHFR SNP among a handful of other possible genetic mutations, it is likely that you will be a slow methylator.
HNMT is the first step in the intracellular (within the cell) histamine breakdown pathway and it is important that it is running properly. Especially if you are dealing with any of the microbiome imbalance issues from the first root cause driver due to the possibility that the DAO pathway is offline from gut damage and inflammation.
I’ve been trying to work out the best approach – meaning the most affordable with the most data – and I have been recommending that in cases where we need this data to run the Ancestry DNA. Then take that raw data and upload it into Stratagene here. This will give you the most comprehensive and easy to digest view on your genetics and how they are impacting your histamine intolerance.
I don’t recommend this test frequently as I find that functional labs – meaning what is actually happening in the body NOW and not so much your genetic predisposition – meaning what could happen – is a better place to focus but when we need genetics to support treatment this is the way to go in my opinion.
How to Approach Histamine Intolerance Testing
Identifying histamine intolerance and uncovering its root cause can be challenging, but it’s absolutely possible with the right strategy. While there’s no single perfect test for histamine intolerance, combining clinical evaluation with targeted functional testing can offer clear direction.
A low histamine diet remains the gold standard for assessing whether histamine is driving your symptoms. From there, functional tests like organic acids testing (OAT), advanced stool analysis, nutrient assessments, and genetic panels can help uncover underlying issues such as gut microbiome imbalances, mast cell activation, nutrient deficiencies, and methylation problems.
Remember, testing is just one part of the picture. A systematic, root-cause approach is key to achieving long-term relief from histamine-related symptoms.
Leave a comment below if you have any insights!
References & Resources
- Histamine Intolerance—The More We Know the Less We Know. A Review
- Histamine and Histamine Intolerance
- Evaluation of Serum Diamine Oxidase as a Diagnostic Test for Histamine Intolerance
- the Complete Microbiome Mapping stool test from Nutripath.
- Organic Acid Test from Mosaic labs
- Seeking Health
- Ancestry DNA
- Stratagene here
1 comment
Hi Todd, just wanted to say that your articles are all so informative & interesting, thank you!!
I wish I could work with you but am in the UK. Am trying to tackle histamine, salicylate issues, MCAS. I made a lot of progress through diet changes & some herbs, but then mould exposure set me back. All my problems began after an infection/ antibiotics, and I think there is a genetic element too. Really grateful that you are sharing your insights.