The Top 12 Autoimmune Root Causes​

“Illness doesn’t just happen; illness has causes, so to resolve illness, find and resolve the causes.”

– Lee Cowden, Integrative MD & Lyme Expert

Thanks to the empowering science of epigenetics, which literally means ‘above the genes,’ we now understand that environmental factors account for about 90% of your risk factor for the development and perpetuation of autoimmune conditions, and even the CDC confirms that your genes account for merely 10%.1 And, thanks to groundbreaking research done by Alessio Fasano, MD and his team, we now have an autoimmune equation: a genetic predisposition + environmental factors + a leaky gut.2

The excellent news that follows, is that if you find and remove those environmental factors — aka, your root causes and heal your gut, you have the equation for reversing autoimmune disorders.

So now we’re left with the big question:

What ARE the top autoimmune root causes?

After I beat a two decade course of MS, I quit my corporate job to study autoimmunity full time. After getting certified as a Functional Medicine Health Coach I began to guide and support people back to good health. As people healed I noticed a pattern: when they changed their foods, reduced their load of toxins, rebalanced their guts, and lowered their stress, their hormones came back into balance, symptoms faded, and then disappeared. When I sat down to write a book, a word emerged that represents all the big root cause categories: F.I.G.H.T.S.,™ which stands for Food, Infections, Gut health, Hormone balance, Toxins, and Stress: 

Today, in my Functional Natural Medicine practice I collaborate with Naturopathic Doctors who specialize in resolving the big root causes of autoimmunity. While not everyone has the same specific root causes, there are common F.I.G.H.T.S. factors we see time and time again. The hugely hopeful news is that when our clients address these root causes, they heal. And you can too by using this as a checklist.

The Top Twelve Autoimmune Root Causes

Low Vitamin D

Low vitamin D (<30 ng/ml) is linked to autoimmune disorders, heart disease, cancer, dementia, and worse outcomes of Covid-19. Many factors can contribute to vitamin D deficiencies, including age (over 65); darker skin pigmentation; limited sun exposure; and in some cases, like me, a SNP (genetic mutation) in the D receptor site gene, called a “VDR.” What can you do? Know your number and get your levels up to 70-100 ng/ml to reverse or prevent autoimmune conditions.


A 2002 review in the New England Journal of Medicine, arguably the most well-respected scientific journal, listed 55 diseases that can be caused by eating gluten, including osteoporosis, inflammatory bowel disease, anemia, cancer, rheumatoid arthritis, lupus, multiple sclerosis, and many other autoimmune diseases — and that was 21 years ago!3 More recent research shows that gluten creates a leaky gut in anyone who eats it. Read more HEREWhat can you do? If you are have or want to prevent an autoimmune condition, gluten has to go for good.

Cow Dairy

Drinking cow’s milk has been associated with an increased risk for numerous autoimmune diseases including multiple sclerosis, rheumatoid arthritis and Type 1 diabetes.4 About 75% of people who are sensitive to gluten are also sensitive to cow dairy. What can you do? Remove all animal dairy for 30 days and try it again. If you experience any symptoms, keep it out for 6 months and try again (or not). If you have trouble with cow dairy, replace butter with ghee — clarified butter, which is casein, lactose, and whey-free. Maybe you’ll be able to tolerate sheep, goat, and donkey milk (Seriously. It’s expensive but well tolerated and found in the freezer section of some natural food stores).

Sugar & Processed Foods

A study from 1973 found that sugar in ALL its forms (glucose, fructose, and sucrose) weakens the immune system, hampering the ability of white blood cells to destroy dangerous invaders like viruses and bacteria. This weakening begins within thirty minutes of eating sugar and lasts for five hours. Autoimmunity is an immune system problem so why knowingly weaken your immune system? 5 Ultra-processed foods like chips, french fries, cookies, cake, and pie promote obesity, metabolic syndrome, diabetes, cardiovascular disease and susceptibility to autoimmune disorders.6 What can you do? Ditch the sugar and ultra processed foods. Replace sweeteners with organic stevia, monk fruit, and/or birch (not corn)-based xylitol. For the healing phase, opt to make your own autoimmune Paleo (AIP) snacks and desserts. You might use the mantra: Nothing tastes as good as feeling healthy feels!


We are supposed to have some Candida (fungus also known as yeast) as part of a balanced microbiome. Overgrowth of Candida albicans is a huge culprit in the development of a leaky gut, autoimmune conditions, and chronic fatigue. Common causes of Candida overgrowth include: a sugar-heavy diet (e.g., fruits, starches, alcohol, and ultra-processed foods), antibiotics, steroids, birth control pills, and mycotoxins (mold byproducts) from water damaged building(s). What can you do? Remove the sources that feed and perpetuate Candida. You literally have to starve the yeast with an anti-Candida diet (AIP is ideal). Then add two antifungal herbs, like oil of oregano, oregon grape root, caprylic acid, undecylenic acid, and/or berberine. If Candida is long-standing or body-wide, you may require antifungal medication in combination with the herbs for optimal outcomes.


As with Candida, healthy microbiomes typically host some forms of non-pathogenic parasites. However, growing scientific evidence suggest that parasites may be a big infectious environmental trigger for autoimmune disease. Common parasitic culprits include microscopic amoeba like Toxoplasma gondii, Blastocystis hominis, and Giardia; and helminths, which include worms like roundworms, tapeworms, and whipworms. Parasites harm humans in a variety of ways including wrecking the gut lining, causing major abdominal pain, eating your nutrients, amping up the immune system, and releasing toxins that create wide-ranging symptoms. If you ever had food poisoning, travelers’ diarrhea, eaten from a salad bar, had sushi, or had a pet or a partner, you may be dealing with parasites. What can you do? Like Candida, parasites are notoriously difficult to test for as they attach themselves to the gut wall (or inside the liver or bile duct) and rarely come out on a stool test. The best parasite test in the US is ParaWellness Research, a direct-to-consumer, no-frills test in which the founder still examines samples under a microscope. Frustratingly, you may have parasites even if your test comes back negative. You can bypass testing and do an experiment of organic mimosa pudica seed, a gentle parasite remover. If you see specks, flecks or stringy things in your stool, these may be parasite pieces. Keep going. In our practice we typically treat parasites with both herbs and targeted medications.


Growing scientific research connects mold exposure with various health conditions including headaches, autoimmune conditions, dementias, and cancer. If you have had any water damage in your home, your college dorm, office, car, or childhood home, and you are dealing with headaches, cognitive impairment, sinus infections or congestion, rashes, histamine issues, and/or insomnia, you may be dealing with mycotoxins, persistent tiny toxic byproducts of mold that lodge in human cavities like the sinuses and intestines. Common places that mold grows include window sills, under sinks, in the washing machine, and inside the HVAC system. What can you do? Get your home tested with an ERMI dust (not air) test. Consult with a good home inspector who knows what mycotoxins are and how to look for troublesome moisture in wall cavities, behind shower walls, and in the HVAC unit. If the inspector also does remediation, run, since that’s a clear conflict of interest. If you are sick from mold you must remove yourself from the source of mold. We help people recover from toxic mold exposure with a combination of antifungals, sinus treatment, gentle binders, and liver support.

Lyme & co-Infections

Lyme (Borrelia burgdorferi) and tick-borne co-infections, notably Bartonella and Babesia, is known as “the great imitator” because it mimics many other conditions, including lupus, rheumatoid arthritis, heart disease, Alzheimer’s, and MS. In a weakened immune system, Lyme can become chronic, hidden, and cause mysterious and debilitating symptoms like cognitive problems, migrating joint pain, numbness and tingling, fatigue, dizziness, tremors, tinnitus, visual changes, and cardiac symptoms. What can you do? If you suspect Lyme it’s ideal to work with a natural medicine doctor who knows when and how to best treat it. Healing from chronic Lyme requires a holistic approach and I am fortunate to collaborate with a naturopathic Lyme expert. Together we offer holistic treatment protocols for clients in the US over Zoom. To find a provider near you, sign up for the International Lyme and Associated Diseases Society.


A study by researchers from the University of Michigan claims that even at levels considered to be safe, mercury exposure may be hazardous to health, raising the risk factor for autoimmune disorders among women of childbearing age.7What can you do? Minimize consumption of big fish like tuna, swordfish, and orange roughy and explore having your silver amalgam (which are 50% mercury) fillings removed safely by a holistic dentist. A big word of caution: removing mercury fillings before your body is ready to detox is dangerous, as mercury vapor is lipid soluble and can both cross the blood-brain barrier and lodge in body tissues. Please make sure your gut, which includes your detox organs, is optimized first. This means that you are pooping daily and voiding completely. Also note that chelation treatments like IV or oral chelation are too harsh for many people. Gentler mercury detox strategies include modified apple pectin, chlorella, cilantro, and infrared saunas.


Glyphosate, a powerful herbicide (weed killer) and active ingredient in RoundUp®, is the most heavily used agricultural chemical in the history of the world.8Studies show that glyphosate causes a  leaky gut and increases the risk of many diseases including autoimmune disease and cancer. 9 It is sprayed on conventionally-grown produce and those grains are fed to conventionally raised animals. Glyphosate is also genetically engineered into GMO seeds. What can you do? Consume wild, biodynamic, or organically grown and raised produce and animals; and avoid GMO products. Sadly, even small, organic farms get some side spray from factory farms, so you have to do what you can to support small farms and protect your health. Studies show that eating an all organic diet can lower your load of non-persistent chemicals in just one week.10

Chronic Stress

Chronic stress is the unrelenting type of stress that continues, like ongoing relationship or work issues or abuse, financial pressures, or social isolation. Chronic stress is toxic and alters body chemistry in ways that can harm your immunity, contribute to inflammation, early aging, and autoimmune disorders.11 12 What can you do? Prioritize your emotional wellbeing above all. Start by getting better sleep, doing more conscious belly breathing, and moving your body. Decide to surrender your stressors by letting go of what you can’t control and make a plan to better address each stressful factor in your life. Try tapping, listening to binaural beats, and spending more time in nature

Unresolved Trauma

Simply defined, trauma is a wound that persists. A massive study called ACEs (short for “Adverse Childhood Experiences”) conducted by the CDC and Kaiser Permanente in the 2000s demonstrates links between physical, emotional and mental trauma experienced in childhood and later development of autoimmune disorders. The higher the ACE score, the greater the risk of autoimmune conditions, cancer, Alzheimer’s, and even early death. Just two ACEs is linked with a 70% increased risk of multiple sclerosis (MS), type 1 diabetes (T1D), Hashimoto’s; an 80% greater risk of eczema, IBS, and asthma; and 100% greater risk of rheumatic diseases like lupus, Psoriatic Arthritis (PsA), and rheumatoid arthritis (RA). Did you experience childhood mental, emotional or physical abuse or neglect? Or do you believe you have PTSD or unresolved emotional pain? The issues stay in the tissues until you allow them to come up and out. What can you do? There are many things you on your own: soft belly breathing, journal and draw, shake and dance, try tapping, and/or use guided imagery & hypnosis. There are many trauma healing modalities you can pursue with a skilled trauma therapist: EMDR, trauma therapy, somatic experiencing (SE), trauma release exercises (TRE), breathwork (holotropic, etc.), and psychedelic-assisted psychotherapy (e.g., MDMA, psilocybin, and ketamine under the supervision of a well-trained guide).

It’s a long list for sure, but take heart in knowing that every single one of these culprits is overcomable. We see people transcend their autoimmune disorders every single week. The key to healing is to find and remove your sources of inflammation and lower your toxic load. The great news is that when you take steps to lower your toxic load in any one category, you will be unburdening your immune system, reducing symptoms, and regaining energy and vitality. The idea is to gain more margin in your toxin bucket. That way your immune system is freed up to tackle the stealthy, opportunistic viruses like EBV and bacterial infections like Lyme, naturally.

Here’s a summary of autoimmune root cause reversal:

  • Optimize your vitamin D levels ideally to 70-100 ng/ml to reverse or prevent autoimmune disorders.
  • Go autoimmune Paleo (AIP) with a rainbow of organic vegetables, 100% grass-fed (pastured) meats, small wild fish, and nourishing fats.
  • Remove inflammatory toxins—including Candida, parasites, mycotoxins, and mercury.
  • Address stress and childhood trauma. Prioritize your emotional wellbeing with daily relaxation practices and trauma release modalities that work for you.
  • Embrace foundational elements like getting eight or more hours of sleep, moving throughout the day, pausing to breathe or meditate, connecting with supportive people, and spending more time in nature.

For more guidance, grab a copy of my book: Beat Autoimmune with a powerful foreword by Functional Medicine pioneer, Mark Hyman, MD.

Which root causes do you believe you’re dealing with and what are you doing to resolve them.

Always in your court!

P.S: Want my help reversing an autoimmune condition?

If you live in the continental U.S. and are ready, willing, and able to invest in your best health, I offer Functional Medicine Total Health Transformation Programs over Zoom in collaboration with a skilled naturopathic doctor (ND). Get on my calendar for a free 30-minute discovery call.

1 CDC: Exposome and Exposomics Reference
2 Fasano A, Shea-Donohue T. Mechanisms of disease: the role of intestinal barrier function in the pathogenesis of gastrointestinal autoimmune diseases. Nat Clin Pract Gastroenterol Hepatol. 2005 Sep;2(9):416-22. doi: 10.1038/ncpgasthep0259. PMID: 16265432.
3 Farrell, R.J. & Kelly, C.P.; Celiac sprue; N Engl J Med. 2002 Jan 17; 346(3):180-8; Reference
4 Cordain, L. “The Adverse Effects of Milk”; Reference 
5 Sanchez, A., et al.; Role of Sugars in Human Neutrophilic Phagocytosis; American Journal of Clinical Nutrition; Nov 1973; 261:1180-1184; Reference
6 Reference
7 Reference
9 Samsel, A.; Seneff, S. Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases. Entropy 2013, 15, 1416-1463. Reference
10 Organic diet intervention significantly reduces urinary glyphosate levels in U.S. children and adults. Reference
11 Sheldon Cohen, et al., Chronic stress, glucocorticoid receptor resistance, inflammation, and disease risk.
12 Mariotti A. The effects of chronic stress on health: new insights into the molecular mechanisms of brain-body communication. Future Sci OA. 2015 Nov 1;1(3):FSO23. doi: 10.4155/fso.15.21. PMID: 28031896; PMCID: PMC5137920.




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Palmer is a certified Functional Medicine Health Coach who has helped thousands of people reverse autoimmune conditions based on her own two-decade battle to successfully beat multiple sclerosis (MS). She’s the author of the Amazon #1 bestselling book, Beat Autoimmune, which has a powerful foreword by Functional Medicine pioneer, Mark Hyman, MD.

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