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Natural Treatment and Reversal of Autoimmune Disease

Updated: Feb 24, 2023

We are starting to learn more and more about these diseases and what contributes to their development in otherwise healthy individuals. We now understand that addressing nutrition, diet, stress, toxicity and the microbiome can be pivotal in gaining long-lasting remission of symptoms in many cases.

Autoimmune diseases such as lupus, scleroderma, Sjogren’s, rheumatoid arthritis, psoriasis, psoriatic arthritis, Hashimoto’s, Grave’s, Multiple Sclerosis, Crohn’s disease, ulcerative colitis, ankylosing spondylitis and others do not always have to be a life sentence. We are starting to learn more and more about these diseases and what contributes to their development in otherwise healthy individuals. We now understand that addressing nutrition, diet, stress, toxicity and the microbiome can be pivotal in gaining long-lasting remission of symptoms in many cases.

  • What is autoimmune disease?

  • What causes autoimmune disease?

  • Naturopathic Treatments for all autoimmune disease.

  • How we can help

What is autoimmune disease?

Autoimmune diseases are a classification of conditions which are the result of a dysfunctional immune system. The same immune system which protects us from foreign invaders such as pathogenic bacteria and viruses becomes confused and begins to attack our own tissues and cells which creates damage to certain organs and eventually, loss of function. The specific name of the autoimmune disease depends upon which tissues and organs are being damaged. In Type 1 diabetes, the beta cells of the pancreas which produce insulin are the unfortunate target. In rheumatoid arthritis, the synovium, or lining of the joints as well as in severe cases, some organs are under attack. In Hashimoto’s thyroiditis, the cells of the thyroid gland which produce thyroid hormone are destroyed and can eventually lead to hypothyroidism (low thyroid function).

What are the symptoms of autoimmune disease?

Common symptoms of many autoimmune diseases include:

  • Severe fatigue

  • Pain, stiffness, soreness of the joints and muscles.

  • Stiffness tends to be worse in the mornings and after sitting or lying and improves with movement.

  • Weight loss (but sometimes weight gain)

  • Brain fog, clumsiness, cognitive changes

In general, the symptoms largely depend on the autoimmune disease and the exact tissues and cells being damaged. Those developing multiple sclerosis will have neurological symptoms such as muscle weakness and spasms, cognitive difficulties and mood changes as the immune system damages the myelin sheath protecting the nervous system. But those developing psoriasis present with skin rashes which are difficult to treat and sometimes joint pain as well.

If you are having symptoms which cannot be easily explained, it’s important to see your doctor and have a consultation and exam to help identify the cause. Special blood testing can help identify possible autoimmune disease. Sometimes autoimmune disease can come on quickly, over the course of few months, other times it can occur slowly over the course of several years. Women tend to be affected more than men.

What are the potential causes of autoimmune disease?

Autoimmune disease is often described making the immune system the “enemy”, but in naturopathic medicine, we do not think this is the case at all. Instead, we think of the immune system as confused and why this is occurring is what we must figure out in order to solve the problem. Certainly, genetics can play a role as autoimmune diseases often run in families but, just because you may have genetic susceptibility doesn’t mean you will develop autoimmune disease. Epigenetics, or factors in our environment play in a key role in whether or not certain genes are activated.

These factors can include:

  • Nutritional deficiencies, in particular essential fats, vitamin D and certain minerals like zinc and selenium.

  • Poor diet high in inflammatory plant oils, processed foods and food intolerances or sensitivities.

  • Stress, either a major stressful event or even multiple, smaller stressful events or a stressful period in one’s life.

  • Toxicity and poor cellular detoxification creating cell dysfunction and resulting in the immune system attempting to correct the problem by destroying the cells.

  • Viral infections can sometimes be triggers.

  • Vaccinations can also sometimes be triggers.

  • Hormone imbalances or sudden hormone changes such as puberty and post-partum can trigger onset.

  • Microbiome imbalances affecting function of the gut-associated immune system (remember, an estimated 70-80% of your immune system is in your gut!)

Getting a Comprehensive Evaluation of autoimmune disease:

  • A comprehensive medical history and a physical exam can help reveal clues to any potential causes or triggers that should be addressed such as stress and adrenal function, past viral infections, vaccinations, or toxic exposures that could be triggering the autoimmune disease.

  • Screening and nutritional labs can help identify nutrient deficiencies and weakened organ systems.

  • Dietary evaluations can help identify inflammatory foods for the individual so they can be removed from the regular diet to improve digestive function, the microbiome and immune function.

  • Additional specialty testing, if needed, can help evaluate hormonal imbalances, toxicity, and microbiome imbalances.

  • Once you have an autoimmune disease, it puts you at a much higher risk of additional autoimmune diseases. It is important to take a proactive approach to prevention as well as screening through blood tests to help quickly identify if another autoimmune disease is setting it.

Common Prescription Treatment for autoimmune disease:

Often the initial prescription for many autoimmune diseases are potent steroids such as prednisone to try and quickly reduce the inflammation while the diagnosis is being confirmed or until more specific medication can be started. These are not sustainable long term, however, as the side effects over time can be detrimental since they are so broad acting on the immune system. Over time steroid medications such as prednisone, methylprednisone and dexamethasone can cause:

  • Osteopenia and osteoporosis

  • High blood pressure

  • Diabetes

  • Cataracts

  • Weight gain

  • Infections

A little more specific but still broad acting medications include hydroxychloroquine (Plaquenil) and sulfasalazine affect immune cell signaling and prostaglandin (an inflammatory substance) production. Side effects of these medications include:

  • Nausea, vomiting, diarrhea and abdominal pain.

  • Skin rashes

  • Vision changes

  • Low blood cell counts.

  • Sensitivity to sunlight

  • Infertility

Methotrexate prevents the body from using folic acid, which is needed to help immune cells grow and divide. Unfortunately, it also prevents other cells in the body from growing and dividing normally. Sometimes folic acid is supplemented with the medication to prevent severe deficiency. Side effects of methotrexate alone include:

  • Increased risk of infections

  • Reduced kidney and liver function.

  • Folic acid deficiency symptoms such as mouth sores, diarrhea, nausea or tingling of the hands and feet.

Biologics are a newer class of medications with multiple various targets of the immune system such as specific inflammatory molecules, immune cells and even substances which lead to production of immune cells. Examples of these medications include Infliximab (Remicade), Adalimumab (Humira), Etanercept (Enbrel), Abatacept (Orencia), cyclosporin, Secukinumab (Cosentyx), Ixekizumab (Taltz), Guselkumab (Tremfya), Ustekinumab (Stelara), Benralizumab (Fasenra) and Vedolizumab (Entyvio), but there are others too. Side effects of biologics include:

  • Increased risk of infections including serious viral, bacterial or fungal infections.

  • Cancer, long term

  • Testing for tuberculosis, HIV and hepatitis is often needed before beginning therapy

Naturopathic Treatments for autoimmune disease

Here we’ll list some of the most common treatments we use to address autoimmune disease and correct the immune system function. Please be sure to check with your physician before trying any of these treatments to help ensure there are no interactions with medications you may be taking and that the treatment is appropriate and safe for you.

Dietary Recommendations

  • Avoidance of individual food intolerances or sensitivities

  • Autoimmune Paleo Diet (AIP) can also be very helpful.

  • Whole foods-based diet high in anti-inflammatory fish oils, fresh fruits, vegetables and pasture raised or vegetarian protein.

Lifestyle Recommendations

  • Reducing stress as much as possible

  • Ensuring good, adequate sleep

  • Exercise, daily, for ideally 60 minutes, and it can be as simple as walking or hiking.

Nutritional Supplements

  • Essential fatty acids such as fish oil, high dose and from a quality brand to ensure there are no toxic metals or other contaminants in the supplement.

  • Vitamin D3, sometimes with K2, dosing is aimed to get serum levels to 80-100.

  • Immune supportive nutrients such as selenium, zinc, or vitamin A. Dosing needs to be careful to prevent toxicity in these nutrients.

  • Probiotics, usually spore based probiotics, to help improve the terrain of the microbiome while we correct the diet,

  • If needed, adrenal support for those who shows signs of adrenal weakness and stress as a potential trigger.


Constitutional hydrotherapy treatments at our office are a great way to support the immune system and speed healing. The treatments are designed to help cellular detoxification and nutrition by affecting circulation and lymphatic flow. You can read more about these amazing and relaxing treatments here.

Acupuncture and Chinese Medicine

Chinese medicine and acupuncture can help by treating the autoimmune disease from a different perspective, balancing the yin and the yang, using needles to affect circulation to various organs and herbal medicines to help relieve the symptoms. Acupuncture treatments can be wildly successful, especially when combined with a comprehensive plan to also address nutrition and deficiencies.

Autoimmune disease can arise from many different factors, so a one-sized-approach isn’t likely to be helpful. Suppression of the symptoms through medications which dampen the immune system also don’t fix the problem and unfortunately create unwanted and sometimes dangerous side effects.

Instead, we suggest and approach to better understand the obstacles to normal immune function and cellular health and this requires an in-depth analysis and plan for specific treatment. We have helped many patients with autoimmune disease reach long-lasting remission by working as a team to uncover these causative factors and obstacles and address them head on.


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