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  • Writer's pictureDr. Brian Lum

Can Seasonal Allergies Cause Stomach Upset?

Updated: Dec 30, 2023

My wife often starts a few young seedlings of spinach, lettuce, and tomatoes in a sunny window before they go outside for the spring.

Recently, when we had a few baby plants in the house, I started having headaches and stomach upset and couldn't find a cause until I spotted a few little sprouts of pollen that had shot up from the baby spinach.

Once the offending plant was moved outside, my symptoms went away.

As a functional medicine doctor, I am used to seeing new patients who have been misdiagnosed for years due to symptoms that don't quite fit the mold of a standard diagnosis.

There are, no doubt, many people unnecessarily suffering because of a misunderstanding of how we think of certain conditions.

wildflowers against a blue sky. text overlay Can Seasonal Allergies Cause Stomach Upset? Functional Healthcare Institute

Unconventional Allergy Symptoms

A stereotypical image of seasonal allergies is a person with a runny nose, congestion, and a sinus headache. But for many, their symptoms do not fit neatly into a diagnosis.

Seasonal allergies only cause symptoms for some when they are under stress, others may only have had allergy symptoms after an accident, pregnancy, surgery or an autoimmune disease diagnosis.

Potential Symptoms Of Seasonal Allergies

  • Anxiety

  • Panic Attacks

  • Depression

  • Brain Fog

  • Fatigue

  • Toe Fungus

  • Recurrent Pink Eye

  • Skin Rashes

  • Digestive Problems

Seasonal Allergies & Digestive Symptoms

Among some of the lesser-known symptoms of seasonal allergies are stomach upset, constipation, diarrhea, GERD, acid reflux, nausea, and stomach cramping.

These digestive symptoms can come with little or no upper respiratory symptoms which is why it can be difficult for these symptoms to be traced back to their source.

The Cause: Histamine

Histamine is released when a perceived threat or foreign substance is detected entering the body.

These foreign substances can be things like dust, pollen, and foods we eat every day.

a mast cell preparing to release histamine into the bloodstream
A mast cell preparing to release histamine.

When a foreign substance is detected, mast cells release histamine to rally your body's healing forces.

In response to histamine release, surrounding blood vessels dilate, increasing white blood cells and blood plasma proteins in that area.

Immune system proteins (antibodies) bind with the invading foreign substance (antigens).

Allergies that cause severe symptoms are a consequence of your immune system overreacting.

This overreaction could be due to many factors but in the case of seasonal allergies, it is usually because the body can't keep up with the number of perceived threats flooding your system.

Histamine Can Cause Stomach Upset

When histamine is released in the gastrointestinal tract, it can cause symptoms like stomach pain, bloating, nausea, diarrhea, and constipation.

Underlying conditions and imbalances can also cause too much histamine to be released.

healthy intestinal bacteria
If this healthy intestinal bacteria is overwhelmed with infection, it can make your symptoms worse

A few examples are small intestinal bacterial overgrowth (SIBO), underlying or low-grade infection, poor diet, heavy metal toxicity, nutrient deficiencies, and food sensitivities.

What is referred to as histamine intolerance or histamine sensitivity is usually a combination of a few underlying factors (like infection, toxicity, and liver congestion).

In a case of histamine intolerance, an individual can become sensitized to histamine-containing foods, histamine-releasing foods, as well as classic environmental allergens.

A common treatment for histamine intolerance is to be on a special diet and take supplemental medication - but those with histamine intolerance will only have moderate success without personalized treatment to address the underlying cause.

Read more about Histamine Intolerance

Histamine & Liver Congestion

Often, excess histamine and underlying infection combine to make allergy symptoms (like stomach upset) particularly severe.

Ideally, your liver would remove any excess histamine caused by seasonal allergies but when it is congested from the strain of an underlying infection, it gets 'behind' at clearing away this excess histamine.

This is why you may have had mild allergies before but now the symptoms are unbearable.

There is a certain threshold, a certain amount of toxin or infection that your body can comfortably handle but once it passes that point your body falls behind and your symptoms drastically change.

This could mean that your symptoms get more severe, you have them more often, you have different triggers or they are a different set of symptoms entirely.

Functional Medicine Testing

When patients have unusual or severe allergy symptoms I generally run a few allergy-specific tests so we can better tailor treatment.

These tests go beyond the complete blood count (CBC) test you may get at your family doctor or a patch test you may get at your allergist's office - functional medicine testing assesses function at a deep level, so we can get to the root of symptoms.

Histamine Testing

This test uses either blood or urine to give us a baseline to measure immune reactivity. This test will also give us evidence that histamine is the real cause of digestive symptoms.

Mycotoxin Testing (Mold Test)

This test looks at 31 different mold toxins in the urine. Mold toxicity is the most common cause of severe histamine overload or intolerance. Even if you don't see or smell mold in your home or workplace it is worth testing for.

Comprehensive Stool Analysis

This test evaluates specific levels of your protective bacteria, identifies possible hidden gut infections, and assesses your ability to digest food. This is an excellent evaluation for anyway who wants to pinpoint the cause and get rid of their symptoms quickly.

Finding The Cause

Both in cases of histamine intolerance and in seasonal allergies - histamine is not really the 'problem.'

The presence of histamine in your body is normal and vital to your health.

The overproduction of histamine is a result of your body trying to protect you. Finding the cause of this overreaction will be the key to lessening symptoms.

Even if your allergies consist of 'normal' symptoms like a runny nose, sinus headaches, and congestion - if they are affecting your quality of life or you are dependent on anti-histamines to get through your day then an underlying condition is probably making your allergies worse.

Addressing an underlying viral, bacterial or fungal infection can not only help improve allergy symptoms but will make you feel better overall.

It is possible to get lasting, natural relief from seasonal allergies. A personalized, evidence-based approach can make the difference between a spring indoors by the air purifier and one outside enjoying the new flowers.

If you would like to speak to me to ask questions about functional medicine, allergies or how I can help you, please schedule a Free 15 Minute Consultation or call or text my office at 913-728-5291.

My clinic offers functional medicine appointments as well as manual chiropractic treatments. I do online consultations for those out-of-state or outside of the United States.


If you think that you may have a medical emergency, call your doctor or 911 immediately.  No action or inaction should be taken based solely on the contents of this information. Nor should you ever delay seeking medical advice or treatment due to the information contained on this Website.


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