The 5 Root Causes of Autoimmune Disease (And How to Start Healing)

What if brain fog, anxiety, and mood swings aren't simply all in your head? What if the health of your mind actually starts deeper in your body, in your gut, in your hormones, metabolism, and your immune system? Well, let me tell you, the connection is real and it affects how you think and you feel every single day. And that's why I created Brain Shaping Academy, a six-week program that shows you how healing your body can help you heal your mind. Brain Shaping Academy relies on the same target nutrition and lifestyle strategies that I've used for 30 years to help my patients improve their mental, emotional, and cognitive health. So if you want to feel calmer, clearer, and more in control and stay sharp and protect your brain as you age, check out Brain Shaping Academy at Dr. Hyman.com. Welcome to Office Hours. This is our dedicated 101 space to go deeper, get clear, and explore what truly moves the needle for your health. I'm Dr. Mark Hyman, and each week we're going to pull back the curtain and share the insights, the research, the lessons that don't always make it into our conversations with guests. Because at the end of the day, you are the CEO of your own health, and for many of you, your family's health too. And you might not feel it all the time, but you have far more power and agency than you realize. I'm glad you're here. This episode is brought to you by Function Health, empowering you to live 100 healthy years with over 160 lab tests for just $365 a year and use the code MARK2026 to get $50 off your membership. Autoimmune diseases are a leading cause of disease and a lot of suffering in the United States. Roughly 80% of people who have autoimmune disease are women, and they're a leading cause of death for women between 15 and 65. And yet, despite how common they are, most people are told two things. One, that it's random, which it ain't. And two, that once you got it, you have it forever. It's your whole life. You can't cure autoimmune disease. And you know what I say to that? Nonsense. What you're hearing from your doctor ain't the good news. And I'm going to tell you what you need to know so you can actually understand this condition, what causes it, and how to handle it, and how potentially even to cure it. When you're having autoimmune disease, your immune system essentially attacks yourself. It's like you're attacking yourself. You think your body is some foreign invader and your immune system starts to attack it. And most doctors think, well, all you can do is suppress the immune system because it's just overactive. It's inflamed. It's attacking your body. But the truth is, I don't really want to manage autoimmune disease. I want to find the root cause and actually resolve it for people. So what if the old concept that doctors have that once you have it, you've got it for life, isn't true? What if it isn't your body malfunctioning, but your immune system is actually responding the way it's designed to, and it's responding to some threat, but that threat is usually never picked up by traditional doctors. Now, those threats aren't random. They're things we know about. They're things you're exposed to every day, the food you eat, the environment you live in, stress. And when you start to look at autoimmune disease through the lens of causes, you can shift the whole conversation and stop being a mystery in some random event and it starts becoming something you would actually understand and begin to change. And that's what we're going to break down today. One of the key drivers behind autoimmune disease is something you're doing every single day, multiple times a day, eating. Now autoimmune disease doesn't mean your body's broken. It's your immune system reacting to something. Your immune system's pissed off and you've got to find out why. And when you understand the triggers or the causes, everything starts to make sense about why your body's overreacting to something and why you're inflamed. Now the reason so many people stay stuck when it comes to autoimmune disease is because of three major mistakes. The first is thinking that medication is the only solution. And to be clear, medication can be helpful. It can be life-saving. It can be necessary. But most of these medications work by suppressing the immune system, not by addressing what's actually causing it to go unawakened. So while the symptoms could improve, the root cause is still there. There's a saying in functional medicine, if you're standing on attack, it takes a lot of aspirin to make it feel better. Take out the attack and then you won't need the aspirin. And that's the same as we think about it in functional medicine with autoimmune disease. The second mistake is that believing that autoimmune disease is incurable, that once you have it, it's something you're going to have to live with forever. And that belief alone can stop people from even looking for answers. But what we see over and over again is that when you identify and remove the triggers, the causes, the immune system can actually begin to rebalance and you can start to regain your health. Which brings us to the third mistake and this is the biggest one, not identifying the root cause because autoimmune disease isn't just one thing. It's a response. If you don't ask why the immune system is reacting in the first place, you end up managing the symptoms instead of actually changing the trajectory of the disease. So from a functional medicine perspective, there are five root causes. There's some combination of these things and it's often multiple things, not just one. It could be food and that could be just inflammatory, poor diet. It can be food sensitivities or allergens or things like gluten, which are more of a significant trigger for autoimmune disease and probably one of the most important triggers out there. Microbes and that's infection. So it could be Lyme disease, ticks, viruses, or it could be the microbiome, which also plays a big role. So food and the gut are pretty central to understanding autoimmune disease because 60% of immune systems in your gut. Another big category, the causes of autoimmune disease are toxins and this can be environmental toxins, pesticides, herbicides, heavy metals, flame retardants, phthalates, PCBs, whatever you name it. These are called autogens. They are toxins that create an autoimmune reaction. And then lastly, there's stress and that can be childhood traumas that trigger immune dysregulation later on in life and lead to autoimmune disease, it can be chronic stress. So stress in itself usually doesn't cause an autoimmune disease, but it certainly often usually makes it works or prevents you from getting better. Let's start with the big one first, food. Food is often the fastest and most powerful place to start. You're eating multiple times a day, which means you're either triggering inflammation and causing it or turning it down every single day. Today's diet looks nothing like what our biology was designed for. We're eating foods that are highly processed, high in sugar, low in nutrients, low in fiber, filled with toxic chemicals. Our bodies were never meant to handle. And over time, that creates the perfect environment for inflammation. But what's kind of even more surprising is that even our staple foods have changed. Take wheat for example. Modern wheat has been hybridized to increase the yield, much more starch in it and to shelf life and also to be drought resistant and have all these benefits, which is great. But in the process, it became way more inflammatory for two reasons. One because it has way more glide in our gluten proteins that are inflammatory. And two because it's super starch and has so much more sugar and sugar can be a driver of inflammation and gut disruption. So it's far more likely to trigger an immune response. So it's not just what we're eating. It's how those foods have fundamentally changed like wheat. So what are the most common triggers in food that we see? Gluten gluten gluten. Someone has an autoimmune disease. It's almost malpractice not to get a celiac panel. I just saw a patient the other day who had been diagnosed by her doctor with Hashimoto's, a very common autoimmune disease of the thyroid. And she was being treated by her doctor with thyroid medication, which was fine, but he never went down the rabbit hole to figure out why she has this problem. And turned out she had full blown celiac disease and was never diagnosed and getting off the gluten. It's very possible her thyroid problem could get better or even correct entirely. Next is sugar and refined starches. These are driving inflammation throughout the body. They foster dysbiosis or imbalances in the gut flora. They create a leaky gut. I mean, they do all sorts of things that damage the gut immune system and trigger autoimmune disease. Dairy is another big one. Our modern dairy is hybridized cows. The casing is very inflammatory in there. It's A1 casing and it can be quite problematic for many people. And so I always gluten and dairy are the top two in my mind. Obviously, any kind of ultra process foods, various food sensitivities, you know, if you have a leaky gut or damaged gut, you just tend to react to many different foods so they can kind of jump on the bandwagon and create issues. So it's important to find out what those are. Now here's what most people don't realize. Even a so-called healthy food can become a trigger if your gut's compromised. The gut connection is critical. Now we're going to go deeper on the microbound later, but this is a huge driver of autoimmune disease. Many of us have it and it's called leaky gut. And what that means is that the lining breaks down in your gut between basically your intestinal contents, poop and food, and your bloodstream. And then poop and food literally leak across that barrier and right across that barrier is 60% of your immune system. And your immune system is there to protect you against foreign invaders and it starts to overreact. And over time, that confusion can turn into your body attacking itself. So if you're struggling with autoimmune disease, what should you focus on? Whole, real, unprocessed food, lots of fruits and veggies, lots of good fats like olive oil, avocados, nuts and seeds, high quality protein, foods that help your gut. Library rich foods with prebiotics in them, fermented foods, polyphenols, all these are critical for feeding the healthy gut bacteria and help with regulating immunity in the gut. Because food isn't just calories, right? It's information for your immune system. So an example of a really great meal if you're having autoimmune would be something like wild salmon, greens, a protein could be like grilled, baked, like a salmon, vegetables, have lots of fiber in the oxidants, mixed leafy greens, arugula, spinach, kale, broccoli, Brussels sprouts, you can have carrots, beets, avocado slices, olive oil. That's a really simple meal, but it's super anti-inflammatory. If you want to have lemon juice and fresh herbs like parsley, cilantro, maybe black pepper, garlic, turmeric, all these things can be very helpful. Even sweet potatoes can be really helpful. So the single most important dietary intervention that I've learned to use in the last 30 years of being a functional medicine doctor is an elimination diet. I like to call it an addition diet because we're actually adding in all the good foods, we're taking out the bad foods or things that are potentially inflammatory. And as part of my practice, I created a diet that was super anti-inflammatory that helped the microbiome that helped bounce blood sugar and was great for autoimmune disease. And I developed it and then I turned into a book called the 10-Day Detox Diet and it's essentially a program we have called the 10-Day Detox Diet and you go to 10daydetox.com and you can learn more about it. But essentially it removes the most common inflammatory foods, gluten, dairy, ultra processed foods, sugar, alcohol, but it also removes grains and beans. Not that they're inherently bad, but they can be problematic for certain people. There's also a more extreme version, which is the autoimmune paleo diet, which eliminates all those things I just mentioned, plus gets rid of nuts and seeds and eggs and nightshades. Now not everybody has to do that. I think most people can start with the 10-Day Detox and see how they do, but I found that extraordinarily effective for arresting or stopping or reducing the symptoms from so many autoimmune diseases. I had a person come up to me at a lecture once when I was at Cleveland Clinic and he said, Dr. Hyman, I did your 10-Day Detox diet and I had rheumatoid arthritis and it went away in 10 days. Is that possible? That's possible. It happened for you. So I think that's the kind of thing people don't understand, the power of food is medicine. There's tens of thousands of molecules that are anti-inflammatory in food that are phytochemicals. They have regular inflammation, they support the immune system, they literally are medicine. They have to choose the right ones though, right? So food is probably the most important place to start. It's something anybody can do. It's free. It's important to try a more strict elimination diet like the 10-Day Detox diet. And not just for 10 days, you can do it for three weeks, three months, three years. It's fine to eat long-term, but the point is that it's really going to reset your immune system and reset your gut and that's the key. Now food is just one piece of the puzzle. There are many other triggers and you have to look at all of them. The next one we're going to talk about are toxins. Now, toxin is the next major trigger. It's one that most people actually overlook it because doctors don't know how to test for them, they don't know how to look at them, they don't know how to treat them. We're exposed to tens of thousands of chemicals in our environment. Pesticides, plastics, air pollution, heavy metals. In fact, many of these chemicals didn't even exist 100 years ago. They were sort of newly invented compounds, 80,000 new chemicals in the environment since the Industrial Revolution. And your immune system has to decide, is it safe? Is this a threat? Like, what do I do with this thing? And for some people, the constant exposure starts to overwhelm the system and these compounds are called autogens, autoimmune inducing toxins. And that's when the immune system becomes dysregulated. Instead of just reacting to a real threat, it starts reacting to everything, including your own tissues. So, a simple example of this is mercury. Mercury is a heavy metal that accumulates over time in the body. It can be from fish, from dental fillings, environmental exposures, coal plants. And some people, it can directly activate the immune system. It can cause inflammation, it can cause leaky gut, it can create this overactive immune system that leads to an autoimmune disease. Listen up. 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And if you're one of the first 1000 people this week, use the code mark 2026 for a 50 dollar credit toward your $365 a year membership. That's function health.com slash mark and use the code mark 2026 today. But the key is not everybody reacts the same way, right? It's important to understand that one person can tolerate a certain level of exposure while another person's immune system becomes highly reactive, which is why toxins aren't always the cause. But for some people, they're a really critical piece of the puzzle. And if you don't look for them, you're going to miss a major driver of what's going on. I had a, I remember, just remembering a patient offhand who had terrible ulcerative colitis, I mean, really bad. And we tried everything in functional medicine, dietary changes, supplements, everything we could think of. And it wasn't working. And he was losing weight and he was having bloody diarrhea all the time and really it was quite serious. And you know, he would have had to go on some pretty heavy duty medication. But I said, you know what, we might be missing something. Let's kind of look and see if there's any toxins in your system. And we found very high levels of mercury and we chelated him. We got his mercury down and his ulcerative colitis completely went away. So that's, that's something that actually is not that uncommon in many of my patients. All right. The third major trigger is the gut and your gut bacteria and your microbiome. This is one of the most important pieces of the entire puzzle because a huge part of your immune system actually lives in your gut. Your gut bacteria are constantly communicating with your immune system. They're helping you understand what's safe, what's a threat. And when that system's balanced, your immune system can stay calm, stay regulated and make appropriate responses to things. But when it's disrupted, everything changes. And today that disruption is so common. Things like antibiotics, poor diet, chronic stress, lack of fiber, processed food, all these things shift the balance of your gut bacteria. And when that balances off, you lose the signals that keep your immune system in check. So instead of being precise, your immune system becomes reactive and starts over responding and gets triggered more easily. And in some cases, it turns against your own body and that's where it all connects back to food because the fastest, most powerful way to influence your microbiome is through what you eat. Every meal is either feeding the good bugs and the good bacteria that regulate your immune system or it's feeding the bad bugs that drive inflammation, which is why diet is just one piece of the puzzle. It's one of the most effective tools we have to start restoring balance in the body. And for many people that are on immune disease, I focus on their gut as a way to treat them. I'll just tell you a quick story of a patient I had at Cleveland Clinic with psoriasis, a terrible autoimmune disease. She was on a drug that suppressed her immune system that cost $50,000 a year. She also had migraines, prediabetes. She also had depression and she also had irritable bowel and reflex. And she was seeing all the best doctors at Cleveland Clinic, the best gastroenterologist, the best neurologist for migraines, the best psychiatrist for depression, the best rheumatologist and so on. And she was just barely getting by. And no one said, gee, what's connecting all these things? Why is her body so inflamed? All these are inflammatory problems. Her gut was a mess. I said, let's start with the gut. So I gave her a whole gut reset. I would call the five-warp program for her. She needed an antibiotic and any fungal to clear out the bad bugs. We gave her probiotics, vitamin D, some fish oil. Not that much really. And we put her on the 10-day detox diet. And in six weeks she came back and she said, Dr. Hyman, I'm all better. I stopped my medications. I said, I didn't tell you to do that. She said, I don't know. I just felt so good. I don't have any symptoms. My psoriasis is gone. My migraines are gone. My depression is gone. My urinal valve is gone. My reflex is gone. And I have lost 20 pounds. So that's the power of helping restore a healthy microbiome. And sometimes it's a very specific method that you have to use, not just changing your diet, but that can be done with a good functional medicine practitioner. The next trigger are infections. And this can be things like Lyme disease, viruses, parasites, even bacteria. And this is where autoimmune disease gets confusing. And in this case, what happens is the immune system is trying to attack the bug, but it also cross-reacts with your body's tissues. So it might be trying to fight Lyme disease, but then it creates an autoimmune response to you. And this happens with COVID, with Lyme disease, with certain viruses. And like Epstein-Barr virus can be linked to, for example, MMS and rheumatoid arthritis can be linked to things like Lyme. And these infections often are latent. They're not like an acute infection. They're lingering at a low level. They keep the immune system in a constant state of activation. And over time, that immune response, well, it can start to misfire. It loses its precision and it begins reacting to your own tissues and attacking your own tissues, kind of like a mistaken identity. And this is not uncommon. This is sort of a common framework for even traditional medicine that understands that the body, it's called molecular mimicry. The body reacts to something that's a foreign protein in a bacteria, but it kind of mimics your body's own tissues and then your body starts to attack your own tissues. So looking for hidden infections is really important and nobody has the same history. No one has the same underlying causes. Even with the same autoimmune disease, you can have 10 different causes. So it's important to really understand that. And you have to look at, let's see rheumatoid arthritis. One person could be gluten. One person could be a parasite. One person could be heavy metals. One person could be the microbiome and leaky gut. So you've got to look at all those things. One person could be cream and chronic stress can trigger an exacerbate rheumatoid arthritis. So you kind of have to look at your particular story and your history, what you're reacting to. One person, it might be food, another it might be toxins, another it could be a hidden infection. And so one size fits all medicine doesn't work. And that's because the triggers aren't the same. The causes aren't the same. You have to treat by cause, not by symptom or disease. And this is such a fundamental principle of functional medicine. It's where medicine goes wrong, which we everybody with the same diagnosis as if they had the same disease and they don't even though the symptoms are the same, the causes are different. Okay, the fifth trigger stress. This is when people underestimate because we often think of stress as just a mental or emotional experience, but in the body stress is deeply physical. It directly implacates the immune system in a whole bunch of ways. It can damage the gut lining. It can increase inflammation. It can disrupt hormone balance, especially cortisol. And when cortisol is dysregulated, your immune system becomes less stable. It's more reactive. It's more sensitive. It's more likely to respond. And here's what makes this especially important today. We're living in a constant state of low-grade stress, whether it's work or sleep disruption or information overload or just being constantly on. Your body doesn't really get a break. And over time, that chronic stress becomes another signal telling your immune system that something isn't right. So just like food, stress isn't the only cause, but it's a powerful amplifier of an aggravated immune system. Take an already sensitive system and push it into full-blown dysfunction. So when you step back and look at all this, the autoimmune disease isn't just one thing. It's not just one cause. It's not just one trigger. It's definitely not random. It's the result of multiple inputs coming together over time. Food, toxins, you've got microbiome, infections, stress, all these things interacting with your biology. And for each person, that combination looks a little different. And that's why there's no one-size-fits-all solution. But here's the key. You may not be able to control every single one of these triggers overnight. I want to leave you with a simple, actionable place to start. First, remove the most common inflammatory foods. Things like highly processed foods, like sugar, gluten, dairy. And if you really want to get to it, I would strongly recommend you do the Tended Detox Diet if you have an autoimmune disease, if you haven't ever tried it. It can't hurt you and it could be a miracle cure. But even small reductions of these things, if you can completely limit them, will help lower inflammation. Although if you really want to figure it out, you've got to kind of bite the bullet and actually do a reset. The second is shift your focus to eating real food. Whole, nutrient-dense foods, get rid of processed foods, build your meals around vegetables, high-quality protein, good fats, lots of fiber. Because your body just doesn't need you to remove the bad stuff. It needs the right raw materials to repair and repounce. The third thing is you've got to learn how to take care of your gut and support a healthy gut microbiome. That means feeding your microbiome with fiber-rich foods, with prebiotic foods, fermented foods, polyphenols, all the colorful compounds in food that actually help fertilize the good bugs. And you want to give your digestive system a chance to heal because the gut is one of the central controllers of the immune system. Fourth, you want to start reducing your toxic load when you can. You don't have to be removing everything overnight. Do your best, right? Smallest shifts matter. Improve the quality of your food, try to eat organic when you can, reduce your exposure environmental chemicals. And you can go to ewg.org to learn about all the wonderful guides on household cleaning products, skincare products, what foods to eat, and ways to really reduce your exposures through all the things that we're exposed to, but we don't even know we're exposed to. And so just be more mindful about what you're putting in and on your body. And lastly, don't exhaust stress. Everybody has stress, but you've got to learn how to manage it. Get some sleep, get outside, create moments of calm during the day. All these things have a meaningful impact on how your immune system functions. And here's the most important part. You don't have to do all this at once. In fact, trying to do everything at once can be overwhelming. So instead, start with one area. For most people, the best place to start is food, because when you begin to change what you're eating, you often start to feel better pretty quickly. And that makes it easier to take the next step and the next step until you've addressed more of the root causes that are driving what's really going on. Remember, autoimmune disease isn't just something you have. It's something your body is responding to. Get some trigger, change the inputs, and you can change your story. What if brain fog, anxiety, and mood swings aren't simply all in your head? What if the health of your mind actually starts deeper in your body, in your gut, in your hormones, metabolism, and your immune system? Well, let me tell you, the connection is real and it affects how you think and you feel every single day. And that's why I created Brain Shaping Academy, a six-week program that shows you how healing your body can help you heal your mind. Brain Shaping Academy relies on the same target nutrition and lifestyle strategies that I've used for 30 years to help my patients improve their mental, emotional, and cognitive health. So if you want to feel calmer, clearer, and more in control and stay sharp and protect your brain as you age, check out Brain Shaping Academy at Dr. Hyman.com. Thanks for joining me for office hours. I love diving into these topics with you. Remember, you are the CEO of your own health and every choice you make can move you closer to healing and vitality. I want to keep these episodes as relevant and useful as possible. So tell me, what do you want to explore next? What questions are you wrestling with? What breakthroughs are you chasing? Share your ideas in the comments on social media or through the link in the show notes. I'm listening. Until next time, keep taking charge, keep asking questions, and keep showing up for your health. Tune in. We'll see you next time on The Dr. Hyman Show. If you're looking for help in your journey, please seek out a qualified medical practitioner. And if you're looking for a functional medicine practitioner, visit my clinic, the Ultra Wellness Center at ultrawellnesscenter.com, and request to become a patient. It's important to have someone in your corner who is a trained, licensed healthcare practitioner and can help you make changes, especially when it comes to your health. This podcast is free as part of my mission to bring practical ways of improving health to the public. So I'd like to express gratitude to sponsors that made today's podcast possible. Thanks so much again for listening.