If you have an autoimmune disease, you have probably heard some version of this:
“Your immune system is attacking your body. Here's the medication.”
And sometimes medication is absolutely necessary.
But there's another question we don't ask nearly enough:
Why has the immune system become so dysregulated in the first place, and are there things we can change that may reduce the inflammatory load driving symptoms?
That question matters.
Because autoimmune disease is not just about genetics.
Your genes may create susceptibility, but researchers increasingly recognize that autoimmunity develops through a complicated interaction between genetics, the immune system, infections, environmental exposures, hormones, intestinal health, the microbiome and lifestyle factors.
And autoimmune disease is becoming increasingly relevant.
Recent research examining U.S. electronic health records estimated that about 15.4 million Americans had at least one diagnosed autoimmune disease, with autoimmune disease substantially more prevalent in women than men. Global data also show increasing incidence for several major autoimmune conditions, including rheumatoid arthritis, inflammatory bowel disease and psoriasis.
So something bigger is going on here than “bad genes.”
And women are getting hit particularly hard.
Autoimmune diseases disproportionately affect women, although the female-to-male ratio varies significantly between conditions. Hormones, X-chromosome biology, genetics, immune-system differences and environmental factors are all being investigated as possible explanations.
Some autoimmune diseases are dramatically more common in women. Around 90% of people with systemic lupus erythematosus and systemic sclerosis are female, while rheumatoid arthritis is also substantially more common in women.
This becomes particularly interesting when we start talking about women's hormones.
Estrogen has complex effects on immune activity.
Depending on the tissue, immune pathway, hormone concentration and stage of life, estrogen can influence inflammatory signaling, B cells, T cells and antibody production.
Which is one of the reasons I believe women's hormone health and immune health should stop being treated as completely separate conversations.
This subject is personal for me.
I was diagnosed with endometriosis when I was young.
Endometriosis is not currently classified as a traditional autoimmune disease, but it is an inflammatory, immune-influenced condition, and research shows women with endometriosis have higher rates of several autoimmune diseases, including rheumatoid arthritis, lupus, Sjögren's syndrome, celiac disease, multiple sclerosis and autoimmune thyroid disease.
Years later, after living in Mexico, I discovered that I had contracted a parasite.
That infection went undetected for years while I struggled with systemic inflammation and an impressive collection of symptoms I definitely did not order:
Migraines.
Digestive problems.
Joint pain.
Eczema.
Fatigue.
Weight gain.
Hormonal dysfunction.
It forced me to stop looking at symptoms as individual fires that needed to be put out and start asking what was creating the environment in which all those fires were starting.
That changed the way I looked at health.
And it's one of the reasons I believe so strongly that women with chronic inflammatory and autoimmune conditions deserve more than symptom management alone.
Let's clarify this because the word reverse gets tossed around very casually online.
You cannot currently claim that diet or lifestyle universally cures autoimmune disease. But autoimmune symptoms and disease activity can sometimes improve substantially when appropriate medical treatment is combined with changes that address modifiable triggers, inflammation, nutrition, gut health, stress and other contributing factors.
Some autoimmune diseases can enter remission.
Symptoms can improve.
Antibody levels may change in certain conditions.
Inflammatory markers may improve.
And quality of life can dramatically improve.
But the goal should not be:
“I will cure every autoimmune disease naturally.”
The better question is:
What is driving immune dysregulation in this person, and which of those factors can we actually change?
That's where I would start.
Your immune system does not operate in a vacuum.
Researchers increasingly recognize that autoimmune disease can be influenced by a combination of environmental exposures, infections, smoking, psychological stress, microbiome changes and other environmental triggers interacting with genetic susceptibility.
This is why I don't love the idea of treating every autoimmune condition as:
“You inherited this. Nothing to see here.”
Genes matter.
But genes aren't the entire story.
Start looking at your total inflammatory load.
That can include:
smoking
poor sleep
chronic psychological stress
highly processed food
excessive alcohol
metabolic dysfunction
certain environmental exposures
chronic or significant infections
intestinal disease
nutrient deficiencies
sedentary behaviour
The goal isn't to live in a bubble and panic every time you touch a receipt.
It's to identify the biggest levers first.
This is one of those topics that used to get labelled “woo-woo.”
Not so much anymore.
A 2024 review from researchers at Harvard examined 68 recent studies on synthetic chemical exposures and autoimmune disease. Associations have been investigated with PFAS, pesticides, bisphenols, solvents and other industrial chemicals, although the strength of evidence differs considerably depending on the chemical and autoimmune condition.
That doesn't mean:
“Your shampoo caused your Hashimoto's.”
It means environmental exposures are now a legitimate area of autoimmune research.
So I think reducing unnecessary exposure is sensible.
You don't need to throw everything in your house into a dumpster tomorrow.
Start with the easy wins:
filter drinking water when appropriate
don't smoke
wash produce
use ventilation when using strong chemicals
reduce unnecessary pesticide exposure
don't heat food in old or damaged plastic containers
choose lower-exposure household and personal-care products when practical
Notice the word practical.
You can drive yourself absolutely insane trying to eliminate every environmental chemical.
Stress isn't exactly helping your immune system either.
Heavy metals such as mercury and lead can affect immune function, and metal exposure has been investigated as one potential contributor to autoimmune processes.
But I would not automatically tell every autoimmune patient they have heavy-metal toxicity.
If exposure history or symptoms raise suspicion, appropriate testing may make sense.
And please do not start chelating yourself because somebody on Instagram told you that your fillings are poisoning you.
That is a medical intervention, not a wellness cleanse.
This is one of the most fascinating areas in autoimmune research.
Infections can sometimes trigger or amplify autoimmune responses through mechanisms including molecular mimicry, activation of autoreactive immune cells and disruption of immune tolerance.
And we're learning more every year.
One of the best examples is Epstein-Barr virus, which has been linked with several autoimmune diseases and has particularly compelling associations with multiple sclerosis. Researchers are also investigating its involvement in lupus, Sjögren's syndrome and rheumatoid arthritis.
That doesn't mean everyone needs a $2,000 panel looking for 47 dormant viruses.
It means that infection belongs in the autoimmune conversation when symptoms and history point us there.
Depending on the person, that may include considering:
gastrointestinal infections
H. pylori
parasites
certain viral infections
dental infections
other persistent sources of immune activation
This is personal for me because my parasite went undiagnosed for years.
Sometimes you don't know what you don't know.
Here is another concept that sounded fringe 15 years ago and now has an enormous amount of scientific attention behind it.
Your gut isn't simply a food tube.
It houses a massive immune interface.
The intestinal barrier has to perform a ridiculously complicated job: absorb nutrients while simultaneously preventing inappropriate entry of microbes, antigens and other substances.
Researchers are increasingly studying intestinal permeability, microbiome disruption and altered gut-immune signaling as contributors to autoimmune disease.
This doesn't mean:
“Everyone with autoimmune disease has leaky gut and L-glutamine cures it.”
But increased intestinal permeability has been documented and investigated across several autoimmune conditions.
So if you have autoimmune disease plus:
chronic bloating
constipation
diarrhea
abdominal pain
reflux
unexplained nutrient deficiencies
significant food reactions
ongoing digestive symptoms
I would absolutely investigate what's happening in the gut.
Read Gut Health and Your Hormones.
Food can be incredibly powerful.
But we need to move away from the idea that there is one universally perfect autoimmune diet.
There isn't.
What works beautifully for someone with inflammatory bowel disease may be completely different from what works for someone with Hashimoto's or rheumatoid arthritis.
I generally start with a whole-food, nutrient-dense, anti-inflammatory eating pattern and then get more specific when necessary.
That usually means emphasizing:
high-quality protein
colourful vegetables and fruit
omega-3 fats
adequate fiber when tolerated
minimally processed foods
adequate micronutrients
stable blood sugar
And dramatically reducing foods that aren't doing anyone's immune system many favours:
ultra-processed foods
excessive refined sugar
repeatedly heated industrial oils
excessive alcohol
From there, you can personalize.
The Autoimmune Protocol, or AIP diet, uses a temporary elimination phase followed by structured food reintroduction.
It usually removes foods including grains, legumes, dairy, eggs, nightshades, nuts and seeds for a period of time.
Importantly, AIP is not supposed to mean:
“Never eat tomatoes again because tomatoes are inflammatory.”
The point is to temporarily simplify the diet and then systematically identify your triggers.
A 2024 scientific review found preliminary evidence suggesting AIP may improve symptoms or quality of life in certain autoimmune populations, including people with Hashimoto's and inflammatory bowel disease, but emphasized that studies remain small and more research is needed.
That is how I would use it.
As a tool.
Not a religion.
Tomatoes, peppers, eggplant and white potatoes are commonly removed during AIP.
Do they cause autoimmune disease?
No.
Could an individual person react poorly to them?
Absolutely.
That's why an elimination-and-reintroduction process is so much more useful than giving every autoimmune patient a lifetime list of foods they're never allowed to eat.
Same idea.
Eggs are nutrient-dense foods.
Some people react poorly to them.
Most autoimmune patients do not need to fear eggs simply because they have an autoimmune diagnosis.
If you remove them during an elimination diet, reintroduce them and find out.
Your body gets a vote.
Gluten deserves its own section because the discussion usually turns into one of two camps:
Gluten is poison.
or
Gluten never matters unless you have celiac disease.
Reality is more interesting.
For someone with celiac disease, gluten avoidance is non-negotiable.
Celiac disease is an autoimmune condition in which gluten exposure triggers an immune response that damages the small intestine.
There is also significant overlap between celiac disease and other autoimmune conditions, particularly autoimmune thyroid disease.
Gluten can also increase release of zonulin, a protein involved in regulating intestinal tight junctions and permeability.
That does not automatically mean gluten causes every autoimmune disease.
It does mean that intestinal barrier biology is real, and gluten may be worth investigating in some people, particularly those with Hashimoto's, celiac risk, digestive symptoms or suspected gluten sensitivity.
My preference?
Instead of arguing about gluten on the internet for three hours, remove it for a period, track symptoms carefully and reintroduce it appropriately when celiac disease has been ruled out.
That's useful information.
Stress doesn't mean:
“You caused your autoimmune disease because you weren't zen enough.”
Absolutely not.
But the immune system, nervous system and endocrine system talk to each other constantly.
Chronic psychological stress can alter cortisol signaling, sympathetic nervous-system activity, inflammatory pathways and immune regulation.
Recent research continues to associate severe or traumatic stress exposure with increased risk and activity of several autoimmune conditions.
And then autoimmune disease itself creates stress.
Pain creates stress.
Fatigue creates stress.
Being dismissed by doctors creates stress.
Not knowing whether you're going to feel functional tomorrow creates stress.
It's a loop.
This is why regulating the nervous system isn't fluffy wellness advice.
It can include:
walking outdoors
resistance training when tolerated
yoga
meditation
breathing practices
journaling
therapy
social connection
appropriate recovery
simply saying no more often
You don't have to become a monk.
You just need moments where your body gets the message:
We're safe right now.
This is where the supplement industry can get a little carried away.
You can walk into the autoimmune section of a supplement store and come out $700 poorer with a suitcase of capsules.
More isn't necessarily better.
I want supplements to have a reason.
Depending on the individual, useful things to investigate may include:
Vitamin D plays an important role in immune regulation, and low vitamin D status is commonly observed in several autoimmune populations.
If levels are low, correcting deficiency makes sense.
EPA and DHA have anti-inflammatory effects and may be useful when dietary intake of fatty fish is low.
Magnesium supports hundreds of enzymatic reactions and can be particularly useful when intake is inadequate.
Selenium plays a role in thyroid hormone metabolism and antioxidant defense and may be particularly relevant in some thyroid conditions.
But more selenium is not better.
Iron deficiency can contribute to fatigue, hair loss, exercise intolerance and thyroid dysfunction.
Ferritin deserves particular attention in menstruating women.
B12 and folate status may be important depending on diet, gastrointestinal health and medication use.
Curcumin has interesting anti-inflammatory properties and has been studied across a number of inflammatory conditions.
N-acetylcysteine helps replenish glutathione and has antioxidant and anti-inflammatory actions.
Maybe.
But “everyone with autoimmune disease needs a probiotic” is far too simplistic.
Different organisms, strains and autoimmune conditions may require very different approaches.
This is why I prefer targeted supplementation based on the person rather than the giant autoimmune supplement starter pack.
Your liver is already detoxing you.
Your kidneys are detoxing you.
Your gut is involved in elimination.
Your lungs are involved.
Your skin participates too.
So you do not need a seven-day juice cleanse that leaves you fantasizing about chewing your own arm.
What I do care about is supporting the body's normal detoxification and elimination systems.
That means:
adequate protein
micronutrients
regular bowel movements
fiber
hydration
sleep
limiting unnecessary toxin exposure
reducing alcohol
supporting metabolic health
Certain nutrients are required for the liver's phase I and phase II biotransformation pathways.
But supporting detoxification physiology is very different from claiming you need to purge mysterious “toxins” every month.
This is where I think Midlife Solutions has an opportunity to bring something different to this conversation.
Women's immune systems and reproductive hormones are deeply connected.
Sex differences in autoimmune disease are striking, and researchers continue to investigate the roles of estrogen, progesterone, testosterone, pregnancy, reproductive transitions and X-chromosome biology.
That means a woman entering perimenopause with Hashimoto's, rheumatoid arthritis, psoriasis or another chronic inflammatory condition may have multiple physiological systems changing simultaneously.
She may be dealing with:
autoimmune inflammation
falling progesterone
fluctuating estrogen
disrupted sleep
increasing insulin resistance
loss of muscle
increasing visceral fat
higher psychological stress
Then we wonder why she suddenly feels like her body has staged a coup.
This is why women's autoimmune health cannot be separated entirely from hormonal and metabolic health.
Yes.
And this is the message I want women to walk away with.
An autoimmune diagnosis doesn't mean there is nothing you can do except wait for symptoms to worsen.
Medical treatment matters.
But so does the environment in which your immune system is operating.
Look at your diet.
Look at your gut.
Look at infections when warranted.
Look at environmental exposures.
Look at nutrient status.
Look at stress.
Look at sleep.
Look at blood sugar.
Look at your hormones.
And then start changing the things that can be changed.
Not because autoimmune disease is your fault.
But because having more levers to pull gives you more options.
And when you've spent years feeling like your body has turned against you, getting some of that control back can be life-changing.
Some autoimmune diseases can enter remission and many people can experience significant improvement in symptoms or disease activity. Diet and lifestyle may help support immune regulation and reduce inflammatory burden, but they should not be considered universal cures or automatically substituted for necessary medical treatment.
Increased intestinal permeability is being actively studied as one factor involved in the development or progression of several autoimmune diseases. Researchers believe gut-barrier dysfunction, microbiome changes, genetic susceptibility and immune signaling may interact, but intestinal permeability is not considered the sole cause of autoimmunity.
There is no universal list. Some people benefit from temporarily eliminating gluten, dairy, grains, legumes, eggs, nuts, seeds or nightshades and then systematically reintroducing them. The goal should be identifying individual triggers rather than unnecessarily restricting food forever.
Early studies suggest the Autoimmune Protocol diet may improve symptoms and quality of life in some autoimmune populations, but research remains limited. A 2024 review concluded that larger studies are needed to determine which patients benefit most.
Stress alone does not explain autoimmune disease, but psychological and physiological stress can influence immune regulation and inflammatory signaling. Research has linked significant stress exposure with increased risk or activity of certain autoimmune diseases.
Yes, certain infections are recognized as potential triggers of autoimmune responses in genetically susceptible people. Mechanisms include molecular mimicry and immune activation. Epstein-Barr virus is one of the most heavily researched examples.
Certain environmental chemicals, including PFAS, pesticides, solvents and some metals, have been associated with immune dysfunction or specific autoimmune diseases. However, associations vary substantially by exposure and disease, and exposure does not prove that a chemical caused an individual's autoimmune condition.
Endometriosis is not currently classified as a classic autoimmune disease. However, immune dysregulation is involved in endometriosis, and research shows women with endometriosis have higher rates of several autoimmune conditions.
Your genes matter.
But they're not the entire story.
Autoimmune disease develops within an incredibly complicated conversation between genetics, hormones, immune function, infections, the intestinal microbiome, environmental exposures, stress and metabolic health.
And that means treatment shouldn't always end at:
“Here is something to suppress your immune system.”
Sometimes that medication is necessary and life-changing.
But we should also be asking:
What is keeping the immune system activated?
What is increasing this woman's inflammatory burden?
What can we remove?
What can we restore?
What can we strengthen?
Because the goal isn't simply to live with autoimmune disease.
The goal is to create the healthiest internal environment possible so your body has a better chance to function the way it was designed to.
Karen Martel is a Certified Hormone Specialist and Transformational Nutrition Coach specializing in perimenopause and menopause support through personalized hormone care, bioidentical HRT, and evidence-based clinical coaching. She leads an all-female expert team that works with health-conscious women in midlife to identify the root causes of hormonal symptoms and build individualized protocols that actually address them. Karen Martel Midlife Solutions serves women who are done being dismissed and ready for care that fits their biology.
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