
By Jennifer Whitmire MS, MEd, MH, CHES, NEP
Autoimmune diseases are tough to figure out, but one thing that’s getting more attention these days is the role toxins might be playing as the root cause. You see, autoimmune diseases happen when your immune system, which is supposed to protect you, gets confused and starts attacking your own body. This causes chronic inflammation, fatigue, and a bunch of other symptoms that can really interfere with life.
What if toxins are part of what’s throwing everything off?
Over the last few decades, autoimmune diseases have become way more common, affecting millions of people. And while there’s no single cause, research is starting to show that environmental toxins—things we’re exposed to every day—could be making it worse.
Toxins are pretty much everywhere. They’re in our food, water, cleaning products, personal care items—you name it. And when they get into your body, they can cause all kinds of damage. They disrupt your cells and put stress on your immune system, which can lead to constant inflammation. I didn’t even mention plastics, microplastics, and other endocrine disruptors.
Now, your body is built to detox naturally, but with how many toxins we’re exposed to today, it’s like your detox system just can’t keep up.
This is especially important if you have an autoimmune disease. Toxins can crank up your immune response, leading to even more inflammation and causing your body to produce autoantibodies (which is just a fancy way of saying your immune system starts attacking healthy tissues).
On top of that, toxins can interfere with your gut health. Ever heard of leaky gut? That’s when the lining of your intestines becomes too permeable, letting toxins and undigested food particles leak into your bloodstream, setting off even more immune reactions.
The bottom line is, we’re living in a world filled with way more toxins than our bodies were meant to process. And if you’ve got an autoimmune condition, this toxic load might be a big part of what’s making your symptoms worse.

Let’s Talk About The Liver
Your liver is like your body’s personal filter—it’s constantly working to detoxify your system by removing harmful substances and waste from your blood. It’s the main player in the connection between toxins and autoimmune diseases.
But here’s the thing: when your body is bombarded with too many toxins, your liver can get overwhelmed. It starts to struggle to keep up, and when that happens, toxins can build up in the liver and other tissues. This buildup contributes to chronic inflammation which can trigger or worsen autoimmune responses.
Leaky Gut and Letting Your Gut Guard Down
Ever heard of leaky gut? It’s when the intestinal lining becomes too permeable and allows toxins, undigested food particles, and even bacteria to leak into your bloodstream. This doesn’t just sound bad—it is bad. When these things sneak past the gut barrier, they can trigger an immune response that may lead to autoimmune disease or make it worse.
Toxins play a big role in disrupting the balance of your gut microbiome, which is why supporting the intestines and keeping them healthy is key to managing autoimmune conditions.

There’s No One-Size-Fits-All
Now, let me be clear—detox isn’t a one-size-fits-all solution, especially when it comes to autoimmune disease. Everyone’s body is different, and what works for one person might not work for someone else. Just like with diet, exercise, or even shoe size, you need a personalized plan.
Detoxing without a plan can actually make things worse, so it’s important to take your individual sensitivities into account. That’s why working with someone who understands autoimmune health is so important. Detox protocols need to be tailored specifically to your body to be both safe and effective.
Common Toxins Linked to Autoimmune Diseases
We’re surrounded by toxins in our modern world, and for those with autoimmune diseases, some of these can be major triggers.
Environmental Toxins
Think about heavy metals like mercury and lead, pesticides, air pollution, and even industrial chemicals. Breathing gas fumes, paint or stain fumes, car exhaust, … can build up in your body over time and lead to inflammation and aggravate your immune system. Over time, this can lead to or worsen autoimmune diseases. Reducing exposure to these toxins and safely removing them so they can be carried out of the body and don’t just move to somewhere worse, like the brain, can make a huge difference in how you feel.
Food and Water Contaminants
What do you know about fluoride? If you have an autoimmune thyroid condition, fluoride is a real concern. It competes with iodine, which your thyroid needs to make thyroid hormones. T4, one of the main thyroid hormones, is actually made of four iodine molecules attached to a protein called tyrosine. Without enough iodine, your thyroid can’t function properly. If you have an autoimmune condition, just switching from tap water to filtered or spring water is a simple, first step.
And it’s not just water—certain food additives, preservatives, and chemicals can also act as triggers for autoimmune flare-ups. Bromide found in most supermarket breads, buns, and cakes and even energy drinks and some soft drinks also interferes with iodine.
Pesticides and toxins in contaminated food disrupt your gut microbiome and weaken your immune function, which is why eating clean, organic foods is key to healing.

Medications
Some medications, like antibiotics, NSAIDs (think ibuprofen), and even certain psychiatric medications, have been linked to autoimmune disease flare-ups or worsening symptoms. It’s so important to advocate for yourself and have open conversations with your healthcare provider about the risks and benefits of every medication. BUT…don’t stop any meds without talking to your doctor.
Also, be mindful of fillers in medications and supplements—things like gluten and corn are commonly used and can trigger inflammation in sensitive individuals. Always check the ingredients!
For me, my thyroid meds contained dyes and corn-both were worsening my autoimmune disease. I switched to compounded and my antibodies dropped.
Lifestyle Factors
What you do every day matters! Smoking, alcohol, and a sedentary lifestyle can build up toxins in your system and raise your risk for autoimmune diseases. These habits slow down your detox pathways and promote inflammation which makes it harder for your body to heal.

5 Ways to Reduce Toxins and Support Detoxification
Given how much toxins can affect autoimmune diseases, it’s essential to reduce your exposure and help your body detox naturally.
1. Cleanse Your Environment
Take a look at what’s around you. Make your own or choose eco-friendly cleaning products, avoid pesticides, and filter your water to remove harmful contaminants. You’d be amazed at the impact small changes like these can have on your health.
2. Eat Clean
- Focus on whole, organic foods. Eat foods that are as close to their original form as possible-apples over applesauce over apple juice over apple flavors.
- Cut out processed junk and avoid chemically-treated foods.
- A clean diet—packed with fruits, veggies, legumes, sprouted grains, plant-based healthy fats, nuts and seeds, and fiber—supports detoxification and lowers inflammation.
- For anyone dealing with autoimmune conditions, I always recommend giving up gluten and dairy and replacing them with WHOLE unprocessed foods, not gf pasta and gf bread. It might sound hard, but trust me, it’s worth it for your healing.
3. Support Your Liver
Your liver is amazing! Give it some love by eating foods like broccoli, kale, artichokes, garlic, and turmeric. Raw fruits and veggies and citrus for extra vitamin C are also great for the liver. These are loaded with nutrients that help your liver work at its best.
4. Nurture Your Gut
The health of your gut plays a huge role in detoxification and immune function. Add probiotic-rich foods like unpasteurized sauerkraut, yogurt, and kefir to your diet to build a healthy gut microbiome. And don’t forget prebiotic foods like onions, garlic, asparagus, jicama, and sunchokes to feed those good bacteria.
5. Minimize Toxin Exposure
Always Read Ingredients!
On everything! Food, Cleaning Products, Deodorant, Make-up, Shampoo, …
Quit smoking and alcohol, choose organic foods, and switch to natural personal care products. And if you must eat animal products, go for organic, grass-fed, grass-finished to avoid the hormones and toxins found in conventional foods.

Remember, detox isn’t something to take lightly—especially if you have an autoimmune condition. It’s important to work with someone who understands your unique needs. If you’re ready to dive deeper and truly support your body, learn more at The Jen Twins Love Your Liver Masterclass, September 30, 3:00 – 4:00 pm ET/noon – 1:00 pm PT. It’s a great way to get guidance on reducing toxins, restoring your liver, and feeling your best. Let’s work together to create a healthier, toxin-free life!
Click here to Register for the Love Your Liver Masterclass. FREE!


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