In this 3rd article in my 5-part series on seasonal allergies, I cover the most common root causes of seasonal allergies – some might surprise you!

Do you suffer from seasonal allergies, and wonder what the root causes are, so you can start to really fix them, once and for all?

In this 3rd article in my 5-part series on seasonal allergies, I cover the most common root causes of seasonal allergies – some might surprise you!

[You’ll find the links to the other articles in this series down at the bottom of this page.]

What causes seasonal allergies?

As we talked about in Part 1 of this series, seasonal allergies – aka hayfever – are caused by the immune system over-reacting to airborne substances entering the respiratory system. This over-reaction then causes the all-too-familiar and unpleasant symptoms of hayfever.

But why does the immune system over-react in the first place?

And why does this over-reaction tend to get worse over time?

To answer these questions, we need to look at the root causes of seasonal allergies.

What is going on behind the scenes that is causing the immune system to over-react to relatively harmless substances like pollen?

The Root Causes

When the immune system is prone to over-reaction to benign substances such as pollen, what has typically happened is that there’s been a long-standing, often subtle and gradual accumulation of irritation of the immune system by various factors. And this irritation causes the immune system to become more and more sensitive and reactive over time, to more and more substances.

And what causes this underlying immune system irritation and subsequent over-reactivity?

It all boils down to this: repeated exposure to substances which damage the gut and overstimulate the immune system.

And that exposure typically comes from 4 main things:

  1. Allergy-aggravating foods
  2. Leaky gut
  3. Infections
  4. Toxins

Each one of these factors, by itself, can lead to chronic seasonal allergies, but most often, it is the combination of these that leads to and then exacerbates allergies, and then makes them worse and worse over time.

Let’s look at each of these in turn.

Allergy-Aggravating Foods

Some foods more readily cause or aggravate seasonal allergies, so learning which foods those are and avoiding them – while simultaneously working on the other root causes – is a powerful and essential first step towards minimizing the symptoms and chronic progression of hayfever.

So, what foods are the biggest aggravators of seasonal allergies?

  • Grains – the worst offenders are the gluten-containing grains, but all grains are allergy aggravators, in large part because of their gut-irritating lectin content. This includes:


  • Dairy – that includes milk, half-and-half, heavy/whipping cream, buttermilk, all types of cheeses, yogurt, kefir, sour cream, cream cheese, crème fraiche, mascarpone, clotted cream, whey, and casein – are big allergy aggravators
    • Note: butter is not allergy-aggravating for most people, as long as it comes from organic, pastured (grass-fed) animals
  • Legumes (beans, dried peas, peanuts)
  • Nuts and seeds, especially if unsoaked (go here for the how & why)
  • Alcohol, esp. beer and wine
  • Nitrate- and nitrite-containing foods (cured meats)
  • Non-organic foods, especially non-organic farmed proteins, and the EWG’s “Dirty Dozen” fruits and veggies

What’s left to eat, you might wonder…

What I typically recommend for healing any health issue and optimizing overall health is a low carb Paleo diet, which is the optimal diet for just about all humans. No joke. This is the way of eating that we were made for, that makes us the healthiest, strongest, happiest versions of ourselves.

That means, wild or organic pastured meats, organic low carb fruits and veggies, and plenty of healthy fats. For more detailed guidance, check out my article What to Eat for Optimal Health.

Eating this way will go a long way towards reducing your seasonal allergies, and improving your overall health, now and for the years ahead.

And for some people, simply eating a clean, low carb Paleo diet is all they need to do in order to get rid of their hayfever once and for all, and achieve optimal health.

But for others, more work is needed.

Leaky Gut

If cleaning up your diet isn’t enough to minimize or eliminate your allergies, what’s next?

Healing your gut.

Pretty much everyone I have ever treated for seasonal allergies over the past 25 years has shown signs of leaky gut, and fixing this underlying problem is essential for most people to achieve a hayfever-free life (and optimal overall health).

You’ve probably heard of leaky gut, but what does it really mean?

Leaky gut, also known as intestinal permeability, is a very common problem where the intestinal lining – which is a thin barrier between the contents of the intestines and the bloodstream – becomes damaged, and the gaps between the cells in the gut lining – called tight junctions – get wider. These larger gaps in the gut lining allow bigger food particles to escape from the intestines into the bloodstream before they’ve been fully broken down.

leaky gut

Since these bigger food particles often bear some resemblance to the larger molecules of pathogens such as viruses, the immune system often thinks these larger-than-normal food particles are invaders, and sets off an immune reaction to protect us from them.

You see, the immune system’s primary job is to protect us from potentially harmful invaders, such as pathogenic microbes, toxins and allergenic substances. To do this, when the immune system finds something that it considers to be a threat within our bodies, it goes into action, launching an immune response to surround, destroy and remove the invaders.

And once an immune response is activated by larger food particles escaping from the digestion into the bloodstream, the immune system is then always on alert for those items to appear again, and when they do, it more readily launches another response. And so, over time, it becomes more likely that the immune system will react, and react, and then over-react, to perceived threats from foods, and also to label more and more sort-of-similar items as invaders.

So how does this all relate to seasonal allergies?

Well, when leaky gut has allowed this vicious cycle of immune system over-reactivity to develop, then the over-reaction to food particles tends to spill over and create an over-reactivity to lots of other things, including the typical triggers of allergies.

tree leaf collage

This is called cross-reactivity. The proteins in seemingly different substances can look a lot alike to the immune system, so once it’s reacting to one, it’s more likely to react to all compounds that have some similarity. Better safe than sorry, the immune system says!

It’s a bit like a protective dog, getting worked up about the mailman, and then, all mailmen and UPS drivers, and then all mailmen and UPS drivers and police, and then all people in uniforms, etc., etc.

So now that you have a little bit better idea of what leaky gut is and how it relates to seasonal allergies, let’s talk about what causes leaky gut in the first place.

The Four Main Causes of Leaky Gut

There are 4 main causes of leaky gut, or intestinal permeability:

  1. Elevated stress
  2. Gut inflammation
  3. Infections
  4. Toxins

Each of these contributes to leaky gut by prying open the tight junctions in the intestinal lining, allowing those larger particles we talked about earlier to get into the bloodstream.

Chronic Elevated Stress

With elevated stress comes elevated levels of the stress hormone cortisol, which has been shown to cause and to exacerbate intestinal permeability.1 And elevated stress can come in a lot of forms, including anxiety, depression, marital or family discord, loneliness/lack of social support and connection, health concerns, work stress, and/or financial strain.

Gut Inflammation

This can be caused by a number of factors, including

  • grains
  • dairy
  • processed foods
  • seed oils
  • insufficient digestive juices
    • stomach acid
    • enzymes
  • medications – especially anti-biotics, acid blockers (Tums, PPIs), and NSAIDs

The last 2 causes of leaky gut, infections and toxins, are also 2 of the primary causes of seasonal allergies.

Infections / Pathogens

As you can probably imagine, having pathogens (disease-causing organisms) in one’s body increases – as it should! – the activation of the immune response. This is, after all, the main job of the immune system, to react to and protect us from these kinds of potentially destructive and possibly deadly invaders!

There are 5 main types of pathogens that trigger an immune response:

  1. viruses
  2. bacteria
  3. fungi/mold
  4. parasites (worms)
  5. protists

Keep in mind that many pathogens live inside of us, all the time – that’s just a fact of life. Many of them are harmless, most of the time.

It’s typically the activation – as is the case with viruses, which can lie dormant inside of us for decades – or overgrowth of pathogens that serves to increase the overall reactivity of the immune system. And this activation or overgrowth then exacerbates – in a now-familiar pattern – our reactivity to all potential perceived threats, including all the typical triggers of seasonal allergies: pollen, dander, dust mites, woodsmoke and mold.

The thing is, latent viruses and overgrowths of other pathogens in our bodies is a surprisingly common, and surprisingly chronic, problem. Most people have some level of chronic pathogen overload in their bodies, at all times. This is because of a number of factors that are prevalent in our modern world, which tend to overstimulate and then weaken our immune systems, and thus make us more vulnerable, including:

  • chronic stress
  • insufficient sleep
  • nutrient-deficient & inflammatory diets
  • antibiotics
  • stomach acid blockers
  • exposure to toxins (more on that below)

So, the surprisingly common problem of pathogenic overgrowths in our bodies is another root cause and aggravator of seasonal allergies.

Now, let’s look at the final main culprit in the development and progressive worsening of allergies.


In our modern world, we are bombarded by a huge variety of toxins, day in and day out, through our air, water and food. And this toxic bombardment contributes to the development and progression of seasonal allergies in ways that all exacerbate the immune system’s tendency to over-react:

  1. They worsen leaky gut by damaging the thin, delicate mucosal layer of the gut lining, allowing more and more problematic substances to get into our bloodstream and cause our immune systems to react.2
  2. As unwelcome and destructive invaders, toxins further inflame the immune system’s reactivity to all potential threats. (And rightly so, because those toxins are trouble!)
  3. Toxins worsen gut imbalances, as contact with toxins damages our beneficial gut microbiota (the good “bugs” that live in us and make up a large part of our immune system).
  4. Toxins increase inflammation, in the gut and throughout the body, which interferes with proper immune system functioning. This then causes the immune system to try to compensate by reacting more and more, to overcome the impediment of inflammation.

So, there you have it – the 4 main root causes of seasonal allergies. Hopefully this article has helped you start to make sense of what is happening behind the scenes, to cause and aggravate your seasonal allergies.

In the next article in this series on seasonal allergies, I go over the best tests to do to determine if you have one or more of the root causes of seasonal allergies: gut inflammation, leaky gut, chronic pathogenic overgrowths, and an overload of toxins in your system.


Also in this series on seasonal allergies:

Part 1: What is it & what are the symptoms?

Part 2: Top 7 Triggers

Part 4: How to Use Basic Bloodwork to Determine the Root Causes of Your Allergies

Part 5: Natural Remedies