A Guide to Rare Autoimmune Diseases

Joyous family of three. Loving and caringThe category “autoimmune disease”, as with almost all other diseases, consists of conditions that run the spectrum from very common to exceedingly rare, and everything in between.  These distinctions are sometimes fairly static, but more often they are rather fluid characterizations that tend to change epidemiologically and demographically over time and across global regions.  Below we examine briefly some pertinent information regarding those autoimmune conditions considered to be rare in terms of incidence (how many cases are diagnosed per year) and prevalence (the overall number of cases at any one point in time) within society.

How many of the 80+ autoimmune diseases are considered rare and why?

There really is no one good answer to this question, but autoimmune conditions can be broken down into those that are more common or more rare than others.  This determination is simply numerical, based on incidence and prevalence (above).  It is also important to know that what is considered medically “common” may not always translate to the lay conception of this term.  That is, while a certain disorder may be labeled “common” statistically, it is often likely to still be diagnosed relatively infrequently in the general population.

Of the 80+ autoimmune diseases known to exist, it might be said that the majority of them are considered rare, which unfortunately also means there is relatively little data out there documenting exactly how rare.  This leads to a cycle of “chicken and egg” uncertainty on the topic.  Certainly, we can count such diseases as multiple sclerosis, rheumatoid arthritis and lupus as more common, with the numbers gradually decreasing until reaching such conditions as anti-NMDAR encephalitis, Cold Urticaria, and Goodpasture’s syndrome, which are decidedly more rare.

Are there some autoimmune diseases that used to be rare but are now very common?

Again, in a certain sense, all autoimmune conditions used to be fairly rare, as it has been noted that many have been steadily increasing in prevalence over recent years.  Whether it is because of a lack of recognition, a lack of existing cases or both, autoimmune diseases such as celiac disease were previously unheard of in most circles, outside clinical specialties.  Today, it is difficult to find anyone who hasn’t at least heard of gluten sensitivity.  And disorders that were relatively prominent before, such as type-1 diabetes, have begun to skyrocket in the population of developed countries.  It is also important to keep in mind that the majority of autoimmune diseases are considerably more common in women, making them relatively rare in males.

One explanation for the large increase in autoimmune disease cases within the developed world involves the hygiene hypothesis, which we have discussed previously in past articles.  Briefly, this line of thinking suggests that the reason for such increases in certain autoimmune disease involves the fact that we may have become “too clean” for our own good.  That is, by becoming so good at antiseptic techniques, antimicrobial treatments and general hygiene, we may have inadvertently caused our own antibodies, left with fewer external concerns, to turn their focus inward, attacking instead those internal tissues that appear similar to outside invaders.  This is a mechanism known as molecular mimicry.

What does it mean to be diagnosed with a rare autoimmune disease from a treatment standpoint?

Unfortunately, many times this means that the condition hasn’t been studied as extensively as more prominent diseases, which in turn means that pharmaceutical companies likely haven’t developed as many effective treatments.  Sometimes, if the prevalence is so low as to not provide a profit incentive to these corporations, there is barely any available research or specific therapies.

However, there is some good news too.  As autoimmune diseases continue to be studied more and more extensively, researchers have found that many treatments used for more common ailments also demonstrate some effectiveness for more rare conditions.  This is based on the common pathology involving antibodies attacking one’s own tissues, despite a lack of complete understanding of the exact mechanisms involved in each illness.

Do the rare diseases have common traits (other than their shared autoimmune status) that could help aid researchers or apply treatments of one disease to others?

Not really, at least on a clinical level.  There is some commonality in that many appear to focus on connective tissues within the body, but this is still a very broad target.  Otherwise, the major connection among all of these 80+ disorders is their shared autoimmune origin.  We can only hope that researchers on the forefront of autoimmune investigation will find other connections in the future that might aid in our understanding and treatment of these conditions.


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.  AutoimmuneMom.com 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 AutoimmuneMom.com 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. Christine Smith says:

    Thank you for sharing this article. I was diagnosed last year with an extremely rare AI disease called “Isaac’s Syndrome”. It has been a very tough year trying different treatments/medications, but thankfully, I have a very smart young neurologist who knew what it was when I came into his office, and has been treating me according to the Mayo Clinic’s protocol. My main medications are Tegretol (anti-seizure medication) to control the peripheral neuropathy, and CellCept (immunosuppressant used in transplant patients) to stop the damage to the myelin sheaths in my arms and legs. It is true that medications normally used for other conditions do work for AI diseases. I can say that I am not feeling normal, but have come a long way from the severe symptoms I had at first diagnosis. There is no cure for Isaac’s, and they really do not know what causes it. I pray that one day, researchers will figure it out so I can be completely cured. For now, it is symptomatic management for me.

    • Katie Cleary says:

      Hi Christine,
      Thanks so much for your comment, and I am so impressed that you found a doctor who diagnosed you fast – that’s so tough with these rare autoimmune diseases, let alone the more common ones like MS and rheumatoid arthritis, among others. Glad things are better than the early days, and I too hope there is more useful research coming in our lifetimes!
      Take care,

    • Gary Rothbard says:

      Hi Christine,

      Thanks very much for writing. I had never heard of Isaac’s syndrome, so I truly appreciate you bringing it to our attention and sharing your story. You learn something new every day. So glad that things have improved and you’re feeling markedly better. You can’t go wrong with Mayo advice and protocols, in my opinion.

      In terms of research and new developments, I’m sure you’re probably aware of this place by now, but wanted to mention this organization: National Organization for Rare Disorders (NORD), which may be of some assistance in finding additional answers. Please keep in touch re: any changes/progress/regress.



      • Christine Smith says:

        Thank you for your kind note, Gary. I have heard of NORD, and I check their site often. Just had a full round of EMG/NCV nerve testing today, so we shall see how I am doing when I go back for the results tomorrow.


  2. Lis Kennish says:

    Hello, I’ve been diagnosed (clinical only) with Sjogren’s and have been reading about Dr Joel Fuhrman’s ‘curing’ a lupus patient. Have you read much about this? I believe diet can reverse many diseases and have become vegan and try to juice daily to see if that makes a difference to my auto immune condition. Would like to hear your thoughts.

    • Katie Cleary says:

      Hi Lis,
      I also 100% believe that food as medicine is real and I feel I am my own data point on that subject. But I would really hesitate to call someone ‘cured’ of autoimmune disease. I think you can reverse the antibodies so that they are negative on blood tests, and you can go into remission from the symptoms — so if those are the definitions for cures, then I’ll agree. I think though, once you have an autoimmune disease, you always have to watch your stress level, diet and other environmental factors because clearly you had the genes and susceptibility to onset an autoimmune disease once, so you’d want to be careful about introducing the same perfect storm to onset a new one. Just my $0.02.

      So glad you are using diet to help – we have tons of autoimmune diet articles because there are so many different ones and it’s a matter of finding the right one that works for your symptoms and to heal your gut. Here’s a link to that page, which also has some other articles about leaky gut, processed foods, etc: http://www.autoimmunemom.com/diet

      Good luck and keep me posted! Take care and hope your symptoms are not too bad and you caught it fairly early,
      founder, AutoimmuneMom.com

  3. Stephanie Olson says:

    Hi. I was diagnosed with Relapsing Polychondritis two years ago after many years of crazy symptoms. Having a name to put on it helps me. I think that having access to the internet community is really helpful when you have a rare chronic illness…I can get reassurance that I am not alone in this struggle. And thank you for this article and site.

    • Katie Cleary says:

      Thanks, Stephanie, for the kind words! I so agree about having a diagnosis, and you are definitely not alone. We’re all in this together.

  4. Hi I just happened to stumble onto this site. I have recently had a rough long hospital stay, after going to the ER a few times. I have been diagnosed with a autoimmune disease, but don’t have a name for it my medical team has narrowed it down to 3 different disease’s they claim to be very very rare as in like 1 in 500,00 and have never seen this type of auto immune case. they have not started treatment cause there not sure, what to start. my hands and feet are black and blue and get worse when I drop them to the floor, I’m also bleeding internally but cant find where the blood is going other then they know its pooling in my hands and feet. I have been having blood transfusions every other day. and my white blood cells are attacking my organs. This issue is very painful and the DR’S are trying to keep me as comfortable as possible. I have had tissue biopsy’s taken which have been sent to a specialist, so for now im sitting and waiting for some answers. Im also showing a lot of vitamin deficiencies some are not even showing up on my blood work which means there so low there not traceable in my blood. If anyone has any advice or have had similar problems I would love to hear of any hope

  5. Hi Dawn,

    So sorry to hear about what sounds like a very frustrating experience. I have so many questions, and a couple of thoughts, but it’s too much to get into here. Please feel free to get in touch by email (above), if you want, so we can discuss it further. Hopefully your docs will be successful in coming up with a specific diagnosis and applicable treatment. Depending on where you are located, I may be able to help steer you in the right direction if you’re looking for other opinions. I hope you are able to start feeling well again soon.

    Take care,


  6. Hi,

    Even though Katie gets the credit for the awesome website, I appreciate you reading the article. Hope it was useful! Feel free to get in touch whenever with any questions or comments, either through here or via my email at the bottom of the article.



  7. Katie Cleary says:

    Thanks, Gary! This website wouldn’t be as awesome without you as the main writer!

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