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List of Autoimmune Diseases and the Pathogens that Cause Them

Posted By Jennifer Shipp | Mar 09, 2023

DISCLAIMER: CONSULT WITH A DOCTOR BEFORE DECIDING ON A TREATMENT PLAN FOR ANY DISEASE.

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BEFORE YOU READ THIS ARTICLE...
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If autoimmune disease is caused by infectious pathogens, and if you can find a way to kill the infectious pathogens where they're living inside the body without harming the patient, then you can cure autoimmune disease...even if Big Pharma says it isn't possible.

Introduction to Autoimmune Disease

Autoimmune diseases have become extremely common. Today, there’s a long list of autoimmune diseases that have been recognized and labeled for diagnosis in conventional medicine. This long list of disease-names makes it hard for people to find truthful information about how to cure autoimmune disease because the reality is that the vast majority of these various diseases are actually an expression of the same general problem that we discuss in greater detail at this link

But let’s talk for a moment about how dividing a disease-state like “autoimmunity” into different disease states that each have a different name makes it hard for patients to find treatments to cure their disease. First of all, many of the diseases in this list (which is constantly growing), are not well-funded scientifically. So-called “rare” diseases aren't funded which means that scientists can’t afford to study them even if the scientist is interested in the disease. 

Also, let’s imagine that autoimmunity is not really autoimmunity. In disease, for example, it’s possible to zoom in and look closely at the disease from a molecular or cellular perspective. And then it’s possible to zoom out, and look at the same disease in terms of tissues and nutrient deficiencies. Some professionals are able to look at connective tissues like the fascia to treat and understand an autoimmune disease. One could zoom out even further and look at things like the autonomic nervous system function, the endocrine system, neurotransmitters and hormone levels in the body. In conventional medicine though, patients are sold on a very rigid view of what’s happening in the body. That view is based on cells, receptors, molecules, and very tiny things that can’t be observed with the naked eye or even with a high school microscope. This “scientific” view of autoimmunity isn’t verifiable by the general public. And this view also hasn’t been widely translated into something concrete and real world that autoimmune patients can use to observe and work with their disease.

As a result, autoimmunity in its varied forms has become a diagnosis that feels very permanent and irreparable. Patients are taught that their autoimmune disease is something that’s happening in parts of the body that are so small that no one has ever seen them. They are, as such, being sold on a theory–a model of a disease– that may or may not be correct. 

One of the basic flaws in this theory of autoimmunity is the idea that the body is destroying itself and there’s no way to stop the body from self-destruction. Psychologically and spiritually for the patient, the impact of an autoimmune disease diagnosis then, is the patient’s acceptance that they are self-destructing. In order to accept the disease, the patient has to accept an identity involving progressive self-destruction.

But this idea that the body self-destructs in autoimmune disease conflicts with one of the most frustrating and ubiquitous confounds in science known as the placebo effect. The placebo effect is essentially an observation of the body’s innate ability to heal itself through nothing but belief in healing. In my research, I’ve encountered statistics claiming that the placebo effect will impact 50-70% of research participants such that these participants will experience effects from treatment even if the treatment isn’t “real”. Of course, these statistics beg the question, “what is a real treatment?” because so many treatments that aren’t real according to conventional medicine, work very well to cure disease in scientific studies. So then, I’m naturally inclined to wonder why patients with autoimmune disease have been offered such an impoverished model of what’s going on in their bodies. If conventional medicine were truly trying to cure disease, patients should be given multiple perspectives and options to follow in terms of healing because, in reality, there are many ways to cure autoimmune disease. 

If you’ve been diagnosed with an autoimmune disease that you wish to cure, this book will outline compelling information about autoimmunity that will help you consider other ways of viewing the symptoms and processes that are causing you discomfort right now. Some of the alternative models of autoimmunity won’t resonate with you. Others will. Though we often recommend that patients work with what resonates with them and keep an open mind about what doesn’t, if you are very ill, find a trusted friend or a family member to discuss your treatment plan to come up with a protocol for healing. Unfortunately, illness can sometimes cause people to make poor decisions for themselves, but loved ones may be able to illuminate a safe path toward healing. Patients who are exhausted or who have been on prescription medications for a long time often tend to gravitate toward treatments that seem the least challenging when, in fact, they need to be challenged in order to heal. 

So let’s get started and begin looking at autoimmunity from some new perspectives. 

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Autoimmune Disease Categories: Mixing It Up

There are a number of ways to categorize autoimmune diseases. In conventional medicine, autoimmune diseases are categorized as 1) Systemic / General or 2) Organ-Specific disease. Other systems of medicine like Traditional Chinese Medicine (TCM) and acupuncture or Ayurveda, in contrast, don’t recognize autoimmunity at all. Rather, in TCM, autoimmunity is viewed in terms of the movement of chi in the meridians. Ayurveda regards the energetic movements and blockages as prana which is breath-based energy. While the meridians are located on the fascia, a smooth, translucent material that covers every muscle, bone, and organ in the body to connect one to the other according to how the embryo developed from a disc into a tube and then finally into a human form, the breath-based prana in Ayurveda might be best understood as alterations in pH that occur throughout the body as a result of how our breath patterns change throughout the day. This might sound overly technical, but most people can understand that a battery requires a positive and a negative pole in order for electricity to flow. In the body, acidic pH tissues and body fluids are negatively charged and alkaline pH tissues are positively charged. 

It’s likely that most of our readers have never worked with either of these systems of medicine, but both are legitimate and useful models of medicine that autoimmune disease sufferers can use to “escape” from the conventional model of medicine that says that autoimmune disease can’t be cured. Both Ayurveda and TCM are widely practiced throughout the world. So, as we begin this discussion, we want to encourage our readers to seek out practitioners of Ayurveda or TCM as a part of their healing journey to find support.

When we write our books, we don’t limit ourselves to one model of medicine. Rather, we look for the points of connection between the various models that we study. If a particular treatment works, we take note and we try to figure out why it works. And the good news is, sufferers of autoimmune disease and cancer have a lot of treatments to choose from to heal themselves. While conventional medicine doctors claim there is no cure for autoimmune disease or cancer, quite the opposite is true. When patients seek out natural treatments for autoimmune disease or cancer prior to exposing themselves to years of pharmaceutical medications, autoimmunity and cancer fall into a category of disease that’s relatively easy to resolve in comparison with, for example, an infection with a high mortality rate that kills people quickly. Autoimmune diseases are supposedly chronic illnesses which means that patients believe they’ll be paying into Big Pharma for their entire lives. And they believe that they’ll get worse and not better over the course of a long period of time. But the fact is, the slow-moving nature of autoimmunity and some types of cancer is one of the reasons why patients with these diseases have so much hope. Patients with a slow-moving disease have time to experiment with natural treatments that do no harm in order to find the treatment that works best for them.

The Barefoot Healer's Guide to Autoimmune Disease, Volume 1 - BUY HERE!

Below, we provide a list of autoimmune diseases and pathogenic infections that have been scientifically correlated with each of them. So we’re stepping off into this material by looking at autoimmune disease as a different type of infection that moves very slowly. The infectious pathogens involved in the development of autoimmune disease are often associated with specific types of “infection”, but they manifest differently because of their location and habitation in the body. 

A lot of scientists today are studying the link between infectious pathogens and autoimmune disease, but this model of medicine, though it’s famous among scientists, is never discussed with patients  in clinics or hospitals. But the idea that an infectious pathogen might cause autoimmune disease symptoms really resonates with a lot of people who suffer with autoimmunity. This model of autoimmune disease is something that most patients are able to easily comprehend, so it makes a good starting point for patients who want to cure autoimmune disease.

Below is a list of the most common autoimmune diseases and the pathogens that have been scientifically linked to each of them. Under each disease-name heading, we provide links to scientific research into pathogens that are likely to be causing the disease by taking up residence in remote locations such as the liver, the gallbladder, the brain, or other areas of the body that are hard to reach using antibiotics that the doctor might prescribe.

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SIDE NOTE about Reactive Oxygen Species Medicines as Broad Spectrum Antibacterial, Antiprotozoal, Antifungal, and Antiviral Medications

If you’ve been diagnosed with an autoimmune disease, the information we present below will only serve to enhance anxiety unless readers know that there are antibiotic medications that are widely available over-the-counter that can kill the vast majority of pathogens listed below. These medicines, known as Reactive Oxygen Species medicines are some of the most powerful treatments that people will work with in overcoming an autoimmune disease. Below, we link to information about each of the various Reactive Oxygen Species medicines so that readers can obtain additional information, but note that often Reactive Oxygen Species medicine is only able to kill pathogens, not protect the body from new infection. 

In the pages that follow, we’ll discuss how to rebuild tissues and organs to make them healthy again and more resistant to the infectious pathogens that are strongly correlated with autoimmune disease. For now, simply note that Reactive Oxygen Species medicines can kill pathogens that cause autoimmune disease. These Reactive Oxygen Species medicines include: 



Read more about the biology of Reactive Oxygen Species medicines here.

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Autoimmune Disease List

Systemic Autoimmune Diseases



Systemic Lupus Erythematosus (SLE)

Behcet’s Disease

Churg-Strauss Syndrome / Eosinophilic Granulomatosis with Polyangiitis (EGPA)

Paraneoplastic Pemphigus



POEMS Syndrome



Relapsing Polychondritis (RP)

Scleroderma



Borrelia burgdorferi / Lyme Disease





Sjörgen’s Syndrome

Organ-Specific Autoimmune Diseases:

Hematologic/Cardiovascular Autoimmune Disorders

Raynaud’s Syndrome Acquired aplastic anemia Acquired hemophilia  Antiphospholipid Syndrome (APS) Autoimmune Hemolytic Anemia (AIHA) Cold Agglutinin Disease (CAD)

Cogan’s Syndrome (CS) Evan’s Syndrome  Granulomatosis with Polyangiitis (GPA) / Wegner’s Granulomatosis

Henoch-Schonlein Purpura / IgA Vasculitis Immune Thrombocytopenia (ITP) / Autoimmune Thrombocytopenia Purpura Polyarteritis nodosa (PAN) Pure Red Cell Aplasia (PRCA) Autoimmune Vasculitis
    • Helicobacter pylori


Gastrointestinal Autoimmune Disorders

Celiac Disease Crohn’s Disease

Ulcerative Colitis Autoimmune Pancreatitis Autoimmune Gastritis

Endocrine System Autoimmune Disorders

Hashimoto’s thyroiditis / Chronic Lymphocytic Thyroiditis / Autoimmune Thyroiditis Grave’s Disease Autoimmune Addison’s Disease

Autoimmune Pancreatitis (AIP)

Autoimmune Polyglandular Syndromes /Schmidt Syndrome / Autoimmune Polyendocrine Syndrome Type II

Type 1 Diabetes

Joint/Muscle/Connective Tissue-Related Autoimmune Disorders

Arthritis Psoriatic arthritis Rheumatoid arthritis (RA) Palindromic Rheumatism Ankylosing Spondylitis (AS) Eosinophilic Fasciitis Immune-Mediated Necrotizing Myopathy (IMNM) Lambert-Eaton Myasthenic Syndrome (LEMS) (rare) Mixed Connective Tissue Disease (MCTD) Polymyositis Polymyalgia Rheumatica  Undifferentiated Connective Tissue Disease



Neurological Autoimmune Disorders

Multiple Sclerosis (MS)

Balo’s Sclerosis  / Concentric Sclerosis (rare)
      • Balo’s disease is said to be a rare subtype of Multiple Sclerosis.
      • Balo’s disease / Concentric Sclerosis patients sometimes spontaneously recover, which suggests that this disease may be caused by a pathogen that goes away when the patient recovers their immune system functioning. Two parasites could be involved as the cause of Balo Disease


    • Tenia solium - About 30% of disorders involving seizures are misdiagnosed as epilepsy. In the U.S. epilepsy is considered to be an incurable disease, but Tenia solium is a treatable infection.




Autoimmune Autonomic Ganglionopathy (AAG)



Chronic Inflammatory Demyelinating Polyneuropathy (CIDP)



Devic’s Disease / Neuromyelitis Optica



Guillain-Barre Syndrome (GBS) Bell’s Palsy



Anti-NMDA Receptor Encephalomyelitis  Acute Disseminated Encephalomyelitis (ADEM)

Myasthenia gravis  (MG)



Paraneoplastic Cerebellar Degeneration (PCD)



Parsonage-Turner Syndrome (PTS)



Small Fiber Sensory Neuropathy (SFSN)

Respiratory Autoimmune Disorders





Dermatologic Autoimmune Disorders











  • Vitiligo




  • Bullous Pemphigoid




  • Dermatomyositis / CREST Syndrome / Limited Cutaneous Systemic Sclerosis




  • Dermatitis herpetiformis
      • Linear IgA Disease (LAD) / IgA Bullous Dermatosis / Chronic Bullous Disease of Childhood


  • Pemphigus foliaceus


  • Pemphigus vulgaris




  • Palmoplantar Pustulosis (PPP)


Hepatic Autoimmune Disorders



Autoimmune Hepatitis



Renal Autoimmune Disorders



Glomerulonephritis (GN)
  • IgA Nephropathy / Berger’s Disease


Ocular/Auricular Autoimmune Disorders

Ocular Cicatricial Pemphigoid



If you read through all of these diseases in one sitting, you may have noticed that there’s a lot of repetition in terms of pathogens that are implicated in the development of various autoimmune diseases.

Some of the articles that we link to above don’t directly link the infectious pathogen to the autoimmune disease, but the fact that this link between pathogens and autoimmunity exists is noteworthy. Autoimmunity is considered to be an overreaction of the immune system and though immunosuppressive drugs can definitely lower a patient’s resistance to infection, creating opportunities for infection that didn’t exist before the immunosuppressive drugs were administered, there are plenty of studies that we link to above noting a direct correlation between autoimmune disease and infection where an infectious pathogen is present even prior to immunosuppressive drug treatment. 

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