Ah-choo! Compelling Research About Allergies and Autoimmune Disease: Immune System, Root Cause, Disease Progression

young woman sneezes on a flower meadowEach year, millions of people suffer from allergies, autoimmune disease, or both.  These conditions can range from relatively mild to severe and debilitating, and patients with either can attest to the effects such disorders, even when occurring at moderate levels, tend to have on one’s health and well being.  Here we examine some of the things that link these two categories of disease together, as well as those that set them apart from each other.

What are the similarities and differences in allergies and autoimmune disease?

Both allergies and autoimmune disease can be considered hyperimmune responses, whereby the body’s immune system becomes supercharged, attacking or responding to substances that shouldn’t normally draw such attention.  Because these two classes of disorders involve a misplaced inflammatory response, they also tend to overlap somewhat with regard to symptoms.  During flares of each type, one may experience common symptoms such as redness, swelling, rash and itchiness.  This is a result of the inflammatory processes occurring during each acute episode, which are similar in some respects, but quite different in others.

The first major difference concerns the precise causes each condition:  allergies, whether seasonal, perennial or specific, are a response to external antigens (substances that antibodies recognize as foreign and attack), such as pollen, dust, peanuts or shellfish, among a host of others.  In contrast, autoimmune conditions are an immunological reaction mistakenly directed at internal antigens (various innate proteins and body tissues) that become targeted as if they were foreign invaders, despite being normal parts of the body.  One example would be the autoimmune reaction seen in rheumatoid arthritis, where certain joint tissues are attacked unnecessarily, resulting in painful inflammation and deformities in some areas.

Another difference between the two concerns the actual mechanisms by which these pathological processes achieve their intended effects.  Without getting too technical, the difference involves the immunological pathways used in each instance.  Most allergies are initiated by a specific type of T-lymphocyte (TH2), and then directly mediated by something called IgE (immunoglobulin E), which is one of five major immunoglobulins/antibodies produced by B-lymphocytes and involved in different immune reactions.  Its activation leads to release of histamine, which causes itching and swelling.  Such a response is commonly known as a delayed hypersensitivity reaction. In contrast, several types of immune cells can mediate autoimmune diseases, but most often they involve a combination of different types of T-cells (T-killers/regulators/helpers/suppressors), sometimes combined with B-cells, which play various roles in the immune response, whether normal or abnormal.  Depending on the condition, one or more immune processes (B- or T-cell mediated) may be responsible, but those above are considered some of the basic mechanisms for each category.

Finally, because the inciting factors are much more readily known and identifiable with allergies, testing and therapies tend to be quite a bit more specific and effective when compared with those for autoimmune conditions.  Even though there are plenty of lab tests and treatments available for autoimmune conditions, the lack of complete understanding regarding disease causes and mechanisms leaves them less amenable to targeted therapies.  While autoimmune diseases are generally diagnosed and treated with relatively non-specific measures (ANA and ESR; steroids and other immunosuppressants), allergies where individual allergens can be identified through testing are often much more readily treatable via desensitization therapies (allergy shots aimed at blunting/removing the allergic response).  However, allergies are also treated with non-specific methods such as antihistamines.

Is the root cause of allergies and autoimmune disease the same?

Common sense based on the above information tells us that there is undoubtedly a connection between the two types of disorders, since they are both the result of dysfunctional immune responses, albeit to completely different triggers.  For a long time the specific way in which these two conditions align with each other and the commonalities between them remained mostly a mystery.  However, in the last few decades, researchers who are starting to elucidate these mechanisms have made significant advances. One line of thinking that has been around for a while, but has recently gained traction within the medical community is something called the hygiene hypothesis.  This possible explanation for one or both categories of disease is based on the idea that through modern medicine and sanitization techniques, people in the developed world have actually become too clean, ridding themselves of evolutionarily protective microbes (bacteria, viruses, parasites), under the assumption that such bugs are purely harmful.

Evidence corroborating this theory includes identification of beneficial gut bacteria (probiotics) and epidemiological statistics that show far less allergies and autoimmune disease in developing countries with less focus on sanitization and the latest antimicrobial techniques, as discussed in this article published in the journal Clinical & Experimental Immunology. The bottom line thinking is that we have, over many years, inadvertently rid ourselves of certain necessary and beneficial bugs, under the mistaken assumption that all of these organisms are dangerous.  As a result, our immune systems find themselves with less to protect against, and turn towards other targets in the absence of traditional ones.  In essence, we have removed harmful antigens and bugs to the point where our immune systems are, for lack of a better word, bored and looking for something to do. And more recently, scientists at the NIH have identified a gene that is believed to control the expression of both allergic and autoimmune reactions.  This gene, named BACH2, may be the first major step in clarifying the connection between the two, as well as the exact mechanisms involved, although our understanding is still quite rudimentary.

Is there a link between seasonal allergies and autoimmune disease onset/progression/flares?

While a link has been fairly well established (though the mechanism remains unclear) between food allergies and autoimmune disease (e.g., gluten sensitivity and celiac disease), the same cannot be said for seasonal allergies, where the same connection is somewhat lacking in the literature.  Still, some work has been done that indeed supports the theory of seasonal allergies influencing and up-regulating the autoimmune response. Much more prominent are patient anecdotes and testimonials, which abound online and clearly indicate some sort of connection between the two.  One story related to me personally involves a woman who had terrible allergies during her last trimester of pregnancy that induced unbearable sinus headaches, and then subsequently developed Hashimoto’s thyroiditis postpartum.  Naturally she is suspicious about there being a connection between the two.

Whether these relationships are correlative or causal – or their exact nature and direction – can’t be accurately determined without scientific experimentation.  Still, such attestations certainly offer evidence that something is going on in terms of a connection between the two.  Patient observations unfortunately must begin to accumulate sometimes before the problem is officially recognized and research action is undertaken.  Therefore, it is crucial for anyone who suspects that their allergies and autoimmune issues are related to continue to report such suspicions to his or her physician, so that we may build evidence for this connection, in the hopes of spurring additional research efforts.

Questions for your doctor:

  • How can I know exactly which things I’m allergic to?
  • Am I a candidate for allergy desensitization?  Why or why not?
  • Can you explain the connection between allergies and autoimmune disease?
  • In your clinical experience, do seasonal allergies have a connection to autoimmune conditions?  What is the direction of that connection?
  • Can you give me your opinion on the hygiene hypothesis and what I can do personally to avoid such unintended consequences of being “too clean”?

About the Author
Dr. Rothbard is a professional medical writer and consultant based in New York City, specializing in medical education articles targeted at a variety of audiences, from children through clinicians.  After leaving medicine, he worked as a biology and medical science educator for several years, before deciding to pursue writing full-time.  He may be reached at [email protected].

This post contains opinions of the author. is not a medical practice and does not provide medical advice, diagnosis, or treatment.  It is your responsibility to seek diagnosis, treatment, and advice from qualified providers based on your condition and particular circumstances.  Camino Real Ventures, Inc., the company that makes available to you, does not endorse nor recommend any products, practices, treatment methods, tests, physicians, service providers, procedures, clinical trials, opinions or information available on this website.  Your use of the website is subject to our Terms of Use and Privacy Policy



  1. You’re very welcome, and please come back often for new articles.


    • Hi I have hashimottos disease was diagnosed 2 years ago but was an allergist who discovered it. I think allergies are related to it I also have not had medical insurance for a year so been taking b12 for it. Does help but still get migraines once in a while. I am a rare case though I am not over weight I am under weight and hyper but also have a sleep disorder. I was on ambien for that which helped but still have no medical insurance so no longer have it, I did figure out when I eat bread products my migraines are more often. But when I take b12 I do feel much better. and also b12 helps with my symptoms of allergies but not sure if they are allergies or the hashimottos but does feel like allergies. Like I said guessing cause I have no insurance anymore just know b12 seems to help,

      • Hi Suzy

        I had a severe Anaphylactic episode a year ago and developed a severe Vitamin B12 Deficiency. I get quite awful symptoms but the B12 injections have relived them. Absolutely fascinating xx

  2. Hi I have hashimottos disease was diagnosed 2 years ago but was an allergist who discovered it. I think allergies are related to it I also have not had medical insurance for a year so been taking b12 for it. Does help but still get migraines once in a while. I am a rare case though I am not over weight I am under weight and hyper but also have a sleep disorder. I was on ambien for that which helped but still have no medical insurance so no longer have it, I did figure out when I eat bread products my migraines are more often. But when I take b12 I do feel much better. and also b12 helps with my symptoms of allergies but not sure if they are allergies or the hashimottos but does feel like allergies. Like I said guessing cause I have no insurance anymore just know b12 seems to help,

    • Katie Cleary says:

      Hi Suzy,
      Thanks so much for your info – are you taking B12 alone or also with thyroid supplement? So curious too how much B12 you are taking. I too have terrible allergies and have to have 3 shots every 2 weeks (maintenance mode after 2 years of shots) to keep all of the symptoms at bay – this in addition to my daily allergy pill.

      Hope you are feeling good since you wrote this and thanks again for sharing your story!!

  3. .
    Is your Child [Allergy] SAD ?

    Today’s Allergy = Tomorrow’s Allergic ASTHMA.

    Allergy is a Cumulative Progressive Allergy SnowBall that begins Rolling at Birth > Gaining Speed ( Frequency ) & Mass ( Severity ) as it Rolls Down Life’s Hill toward Allergic Asthma …

    Disease sequence caused by ALLERGY SnowBall is called ALLERGY March.

    Allergy MARCH = Allergy / Allergic Asthma Parents > Pregnancy / Birth > Eczema ( Food Allergy ) > Colic Baby ( Food Allergy ) > Ear Issue Baby ( Allergy moving to Respiratory ) > Wheezing Baby > Child who “Always” has a Cold i.e. Allergy > Child Rhinitis > Congrat’s You now have Allergic Asthma.

    Pls remember that there are TWO Sides to the Allergy Coin..

    Food & Environmental

    That the Cumulative Progression of Allergy MARCH begins with Eczema and Colic Infant due to FOOD Allergy ..
    before it mitigates to Respiratory / Enviro Allergy with Ear Issues > Wheezing > Child who always has a Cold > Rhinitis > Quite possibly Allergic Asthma.

    While “ Some “ Children do outgrow their Food Allergies ( actually Allergy has just Reinvented itself from Food to Enviro ) ..the Aero-Enviro Allergy Side of the Coin often remains and exacerbates to …

    Thus said, it is Important to Stop & Melt the Allergy SnowBall from Rolling Bigger & Faster to ???

    How ?

    STOP a LifeTime of Masking Symptoms with Pharma ..

    And Target the Source of Allergy by = Building Internal Immune Tolerance to the very Enviro Sources that are causing you to Achoo …

    }} Why not Build Tolerance to 14 Major Aero-Enviro Sources via a GOOy CHEWy Honey Treat ..

    You have Tried EveryThing for your Allergies UnTil Now ..

    May we suggest .. RELIEF

  4. Six months ago I had a anaphylactic attack ( allergy unknown) and three days later I collapsed unable to move my legs. Since then I have had unbearable fatigue, brain fog, numbness and sever nerve pain in lower back down my legs. I have seen almost every kind of doctor an allergist included. They think autoimmune but still not sure which and they do not think there was a link. But how can there not be? I developed an unknown anaphylactic allergy 3 years ago. Allergy testing almost killed me, and results suggest I am extremely allergic to pretty much anything that grows. Now I spend most my days in bed and still undiagnosed.

  5. HI a few months ago I was diagnosed with palindromic rheumatism. I don’t have rheumatoid arthritis, even most Dr’s don’t understand this..anyways I’ve been put on methotrexate and hydrochloroquine. The side effects are horrible which prompted me to do a lot of research since this is very rare apparently. I’ve had severe allergies since I was born. So much so my growth was so stunted I was 3 years old and comfortably running under tables. Today I’m only 1 inch above the legal requirements to be a little person. I believe whole heartedly that there is a huge connection between my allergies and this disease. My diet is so ristricted I can only digested a very limited source of proteins and if it has anything to do with animals, gluten and soy those are huge no no’s, yet I’m not celiac. I am wondering why instead of taking these brutal medication’s why isn’t there a heavy duty antihistamine that can be used? Or has it just progressed too far now. I’m just wondering about alternatives, I understand these meds effect everyone differently and I’m not here to deter anyone from trying this treatment, it’s just my body doesn’t seem to get along so well with this option. I’m not sure if I’m asking a question, reaching out or venting however if anyone knows what I’m talking about I’d love feedback, it gets a tad confusing after a while. Thank you

  6. Suzy Robb says:

    I have been dealing with similar issues and after reading all the posts I want each of you to know I feel deeply for you , and I pray for a healing touch from God .. He is about to move with His power again as He once did when He walked the earth…I pray you all feel His tangible love even now….keep talking to Him . He loves you more than you can imagine. I am waiting for miracles too !

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