The Autoimmune Protocol with Dr. Sarah Ballantyne
15 Dec 2025 · 35 min
Dr. Sarah Ballantyne explains the Autoimmune Protocol, an elimination diet designed to calm immune overactivity in autoimmune disease. A clinical trial of IBD patients saw 73% remission after six weeks. The approach combines strict elimination with careful reintroduction, plus sleep and stress management.
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Welcome to the JJ Virgin Lifestyle show with celebrity nutrition expert, Fitness hall of Famer and four time New York Times best selling author JJ Virgin. JJ is a warrior mom whose knowledge and expertise have helped change hundreds of thousands of lives with over 3 point million podcast downloads and appearances on Dr. Phil, Dr. Oz, the Today Show, Rachael Ray, Larry King Love Whoa, whoa whoa.
This show is about you, not about me. I want to help you find practical, real world ways to dial in your health and mindset so you can finally lose that weight and feel strong and energized. Stop settling for less than your personal best. It's time to find out how to look and feel better than ever. And I'll be right here with you the whole way. Welcome to the podcast. I am going to do a deep dive today. If you are struggling with autoimmune disease, anyone your family, close friends are, you're going to want to make sure you stick with me. I have got Dr. Sarah Ballantine on with me today to really dig into the autoimmune protocol and she is the person who took that information, really made it user friendly because of her own life story. So if you didn't catch my last podcast with Dr. Sarah where I went and did the keto diet, you will definitely want to jump on in there and do that one too because what I did, I actually recorded a podcast with her and said stop, I need to like, I need a lot more time with you. And so I just decided to take one in Focus on Keto and one on Focus on the Autoimmune protocol. And so that's what today's is. And Sarah is uniquely qualified to talk about this because she has a PhD in Medical Biophysics and you're going to hear how she ended up applying this to her own story here. But she ended up really sick, 120 pounds overweight with autoimmune, Hashimoto's and a lot of other problems going on and started to look at how she could fix herself and found the Balliol diet and then found the autoimmune protocol and then went and really looked at how could she make that something that everyone could do. She is the New York Times bestselling author of four books and the creator of thepaleomom.com and is really looking at how to take all of this research here and use it to deal with the chronic diseases that we are facing today and to turn them around. So I am really excited about this interview and also I'm excited about some of the cool things she's giving you as resources because she's giving you shopping lists, recipes guides, everything you need to get started on this. And you can get all of that@jjvirgin.com PaleoMom she has been super duper generous. And talking about generous, I also want to give a shout out to the generous Shell are from the usa. This is my little shout out on the podcast reviews every week. I make a point of shouting out for the latest review and I really, really appreciate these. They make such a big difference for our team morale. You know, we all sit there, we are working, working, working to get as much content out as possible. I have a goal to help a billion people get healthy and take their health into their own hands. And it's not something I can do alone. So I'm bringing on the best experts and then also need your help sharing this message out far and wide. So thank you so much, Shell for this one. Love, JJ Virgin podcast episodes 5 stars. I love all the episodes. Quick, informative and very motivational. I love her products too. I have a lot of food sensitivity, so her protein shakes and bars are perfect for me. All right, welcome back, Dr. Sarah Ballantine. I will not let you le me.
I am always, always happy to be here.
You are a keeper. So if you missed the first interview I did with Sarah the paleo mom, all on keto, all your questions answered, you will definitely want to listen to that. And just a little behind the scenes peek. We were actually doing that podcast and then we got into lectins, then we got into autoimmune protocol and I actually just went, er, can I just have a lot more time with you? And let's just divide this all up and attempt to overwhelm people. And so that's what we did. So make sure you tune into that one. But I wanted to dig in today, Sarah, into the autoimmune protocol and I think it came up because we were starting to talk about like all the confusion out there about nightshades and lectins and all this stuff. And I thought, you know, the easiest thing would be to really dive into the autoimmune protocol diet. So if we could start there and just even say, what. What the heck is this diet in the first place?
Yeah. So just like the name suggests, it is a protocol for people with autoimmune disease, but really what it is is it is a diet and lifestyle intervention that is designed to help people with autoimmune disease regulate their immune system. So our immune systems are what are causing autoimmune disease. They lose the ability to tell the difference between some protein in our bodies and. And a pathogen. So a virus or a bacteria or parasite, and it starts treating something in our bodies as a bacteria that needs to be attacked. And so instead of attacking, you know, that flu virus or whatever it is, it might attack our thyroid or our joint tissue or the myelin sheaths around our neurons. And depending on what your immune system's attacking, that's what makes one autoimmune disease versus another. So that's, you know, if it's your thyroid, it's either Graves disease or Hashimoto's thyroiditis. Is it? If it's your joint tissue, it might be ankylosing spondylitis or rheumatoid arthritis. If it's the myelin sheaths around your neurons, it might be multiple sclerosis. So what's different between all those diseases is just which thing the immune system has gotten confused about. It's not just that the immune system's confused. It's that the immune system can't figure out how to turn itself off. So it's also stimulated to attack because it's seeing your thyroid or your joint tissue or your gut lining or your adrenal glands. Whatever it is, it's seeing that thing as a foreign invader. It thinks it's infected, and it's basically lost the ability to calm itself down and turn itself off. So the autoimmune protocol is basically the optimal diet and lifestyle for exactly that. Turn off the immune system. We can't make an immune system that has learned how to attack something in your body. Forget. But we can regulate the immune system. So it's not in that big attack mode. So it's not actively attacking your tissue and causing damage, which is what causes symptoms.
So can we get a little personal here? Because I know we share something in common. Well, we share a couple things. We're moms.
Yes.
And we're both moms with Hashimoto's and you. I mean, and I'm going to assume, like, here you are, you're a massive researcher, PhD in medical biophysics. And I'm going to assume that you kind of got into this whole thing because of your own personal story.
Yes.
So share that one.
Yeah. So I, you know, it's funny because I did research in inflammation, innate immune activity. I studied something called the systemic inflammatory response syndrome, and then I moved into sepsis and the acute respiratory distress distress syndrome. These are all things that happen in critical care wards when the immune system gets out of control. I moved from that into cell biology. I discovered and characterized a new tumor suppressor gene that was really important for our gut epithelial cell tight junctions. So it was actually a really important gene in how basically our guts are not leaky. And I was doing all of that research in the same way that most research is done with the idea of if you can really understand all of the pathways going on here, you can manipulate those pathways with a drug to save somebody's life. Fast forward to I've had a baby. I am borderline diabetic, I'm morbidly obese. I have a dozen different diagnosed health conditions. And I finally start taking all of that information and understanding, or at least working towards understanding of how does nutrition impact all of these different pathways? How does how much sleep I get or activity or stress level impact all of these pathways? Instead of developing a drug to help the immune system regulate itself, what is the role of all of these other choices that we make throughout the day? And it turns out that the role is huge. The impact of our nutrition, of compounds in our foods, of things like pesticide exposure, heavy metal exposure, all of the lifestyle factors, the cumulative effect of all of those little choices that we make throughout the day on things like hormones, gut health, immune system health is enormous. And so I really was able to take this scientific background that really had nothing to do with diet and lifestyle, and then kind of self teach myself nutritional sciences and basically put those two things together to be able to really understand. Oh, no. When you eat tomatoes, they have this compound and this compound that actually cross the gut barrier and stimulate the immune system. And so if you have an overactive immune system, like I do with Hashimoto's thyroiditis, tomatoes are a terrible food. And so it was really like, it was frustration, right? I was super sick. I have not just Hashimoto's thyroiditis, but two autoimmune skin conditions and fibromyalgia, myalgia. And I just, I was so frustrated. And it was just that moment of, huh, I wonder if it has anything to do with Food.
So glad you asked that question for so many people. You felt. So you asked that question started and how did you like come to the autoimmune? I mean, like, how did you, how did you put this all together?
So the first thing that I found in my searching was the Paleo diet, which I thought sounded ridiculously crazy. And who would want to do that? I had this, the same reaction that most people have when they look at a lot.
I want to remind everyone, Sarah is known as the Paleo mom.
You know, in those days, this was summer of 2011, and in those days there were precisely two books on the Paleo diet. The Paleo Diet from Professor Lauren Cordayn and the Paleo Solution from Rob Wolf. And I think there was.
I learned Paleo from Lauren Cordain in a small room of eight.
I think he also the Paleo Diet Cookbook had just come out that, that summer as well. And it was basically described in those books as, here's all the things you don't eat. And so when I, I first started basically on, on Dr. Google, like so many of us, but I was ahead of my time because it was 2011 and I found an article on Professor Cordain's site that was relevant to one of my autoimmune skin conditions and sort of had this explanation of how the Paleo diet can help. And that was what got my curiosity piqued. So I ended up reading everything that I could, not just Professor Cordain's book and Rob Wolf's book, but also all of the research that they reference. And then that led to reading other medical journal articles. And I just kept kind of going down that rabbit hole. I read everything I could for three months and then decided I needed to try it. I went all in because I'm an all in kind of person. And in two weeks I went off of six prescription medications, one of which I had been on for 12 years. And I started losing weight that I thought I was resistant to weight loss and I would never lose weight. I got to my goal weight, I got fit and things like irritable bowel.
Syndrome went away 120 pounds. I want people to understand it wasn't you lost 10 pounds. Weren't you like 120 pounds overweight or something like that?
At my heaviest, I was 120 pounds overweight. I did lose some weight on a low carb diet before finding Paleo. So Paleo helped me lose like the last 30 pounds, which is also the hardest 30 pounds to lose. So I'm still Super grateful for that. But, like, full disclosure, losing weight and not getting healthy was the frustration that brought me to Paleo. And then Paleo, basically curing almost every. My blood sugars normalized, diabetes went away, my blood pressure was great. I never had another migraine again. My irritable bowel syndrome went away, my asthma went away, most of my allergies went away. Like, it was miraculous. And I became a complete zealot, which is why I had to start a website to have an outlet for my enthusiasm. But also that to me was like, here is the power of diet. Now, here are these things that didn't get better with Paleo. So now that I understand just how powerful diet can be, what am I missing? And it was that question that brought me to the autoimmune protocol, which was originally developed actually between conversations between Rob Wolf and Professor Cordain. Rob was trying to help his mom. And so Professor Cordain had. When the Paleo answer came out, he had a section for autoimmune disease in that book. At the time, he just had an article on his website, and Rob Wolf had, like, half a page. And it was. They both basically said, oh, and by the way, if you have autoimmune disease, you also shouldn't eat these foods. And it was. They had two different lists of foods that were not the same. And then there were, like, two websites that I could find that had taken both of those lists and, like, smushed them together and made one list of, like, oh, and if you have autoimmune disease, here's the foods that you don't eat. And so I was about two months into Paleo, and I'm like, this is amazing. My whole family's going to start doing it. This is fantastic. I'm going to start a website. I'm still writing. I'm learning all the science still, and I'm writing about it. This is really fun. Hey, there's these extra foods I shouldn't eat. Eggs and nightshades and nuts and seeds. Why, like, why are those a healthy food for a regular person and not for someone with autoimmune disease? And so I started diving into the science. There was almost nothing to go on. And writing about it as I was. As I was doing it. So I was Paleo for four months, and then as a New Year's resolution, I went full aip. And then that was when, like, the magic really happened and everything really started to come together. And so I'm like, okay, great. So tomatoes were not my friend. But, like, why I need to understand this. And so what I did was I started writing about the automobile protocol while I was also integrating other concepts. So Dr. Terry Wahls TEDxioCity talk went viral on YouTube that October. And that was a tremendous influence because her whole talk and actually the basis of the Wahls protocol is consuming the nutrients that our mitochondria need to produce energy. But it just so happens that nutrients are required by every system in the body. And our immune system is a huge nutrient hog, I would say even more so than our mitochondria. And if you're deficient in any one of the 20 nutrients that your immune system needs to function, the first thing that the immune system stops being able to do is turn itself off and regulate itself, which is exactly what's happening in autoimmune disease. So I started incorporating that focus on nutrient density into the autoimmune protocol, focusing on lifestyle factors, getting enough sleep, being active but not over training, managing stress, connection, nature, time, all of those things help the immune system function. We've got great scientific papers showing that those lifestyle factors are really critical. Our regulatory aspects of the immune system. The immune part of the immune system, whose job it is, is to kind of keep the system reined in and turn it off once you've finished fighting off that flu virus, are most active while we're sleeping. So if you're not getting enough sleep, your immune system can't regulate itself. And that's why not getting enough sleep is just by itself, inflammatory. And so I was incorporating all of those things. I ended up being offered a book deal, which was a huge honor. And my first book was the Paleo Approach, which is basically the definitive guidebook on the autoimmune protocol. But it was really like, I get credit for creating it, but I didn't. I think I made it more robust. I definitely refined it, but the original concept comes from Rob Wolf and Professor Cordain, and certainly my work popularized it and made that information accessible. And what's super exciting, super user friendly, that's the other thing that I think is really important, because it is a big ask. And so you have to make that big ask as accessible as possible. Especially because the people who need the autoimmune protocol the most are the people who are the most tired or sore and don't have the energy to cook or go grocery shopping. But what's super exciting to me is now we've got clinical trials that are catching up to this amazing experience from the community of other people adopting the autoimmune protocol. And sharing their stories. But there was a the first scientific paper was published last fall and it was in patients with inflammatory bowel disease. About half had Crohn's and about half had ulcerative colitis. And they did a six week gradual transition to the automobile protocol and then five weeks of maintenance. By the end of that six weeks of just a gradual implementation of the automobile protocol, 73% of the participants were in full clinical remission. And they all had increased markers of improved markers that of disease activity. So they all showed reduced disease activity and they continued to improve over the five weeks of maintenance, which is super exciting. And now there's a trial that is ongoing in Hashimoto's thyroiditis.
Oh my gosh, that's crazy.
It's amazing to me that this thing that started out as me just trying to figure out my own health has become. It's become a movement, right? It's sort of within the alternative health sphere, but it is becoming more and more commonly used by I mean, it's already being used by functional medicine and integrative medicine practitioners, but now it's attracting some at least interest from conventional medicine practitioners because these clinical trials are bringing that scientific validity to hey jj, Virgin here.
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Well, and also people are hearing about this, right. So I think there's two sides of it and this is what's so important. Autoimmune drugs suck.
Yes.
And you know you got that piece right.
And they increase your risk. Lifelong risk of cancer.
Yeah. So you've got a horrible option. And then you've got a dietary option option. And now you've got TED talks out, you've got books out, and people are like, oh, there is an option that's, that is a viable option that can completely just drop this rather than these medications that are going to create other.
Problems and not that every person gets off of all of their medications. Like, I don't want to oversell the autoimmune protocol as a miracle cure all. So especially when you have an autoimmune disease that affects organ function, like Hashimoto's thyroiditis, you likely will still need to take some thyroid hormone replacement. You might need less, but.
But you also can drop your auto. Like I still need. I will always have to take thyroid, but I don't have my autoimmune titers up anymore.
The antibodies are right, which is very, very exciting. And what you see, people tend, the drugs that they tend to be able to get off of are the disease modifying drugs. Things like methotrexate for rheumatoid arthritis, or TNF alpha inhibitors or steroids. And those are of course, the ones that do have this increased lifelong risk, lifetime risk of cancer. They're the ones that tend to come with terrible side effects. Sometimes the side effects are worse than the disease that they're trying to treat. Taking something like insulin, if you have type 1 diabetes or thyroid hormone replacement, that is a wonderful, amazing tool that we have that's not just important for symptom management. Our thyroid actually interacts with our immune system. So getting your thyroid numbers dialed in is actually a really important aspect of managing hypothyroidism with the autoimmune protocol. So they're actually really synergistic. But I do want to sort of like you. You might not get off of all of your drug. Like, don't. It's not necessarily going to like replace your doctor. But it is still a very powerful therapy.
What does any. I mean, but here's the thing. You have nothing to lose. This isn't it's, and it's just switching. It's not like you're, it's going to cost you any money because it's not, because you're just trading behaviors, you're just trading the food you were buying. So it's not costing you anything else. And you've nothing to lose. If there's not going to be a side effect here that when you, you know, ate more of the right types of food for you, you had a side effect of, of something bad. The only side effects are side benefits. So there absolutely no reason not to do it.
People who are overweight tend to lose weight. People are underweight tend to gain weight. It's actually a very weight normalizing diet, which is really interesting. It also is a very nutrient dense diet. So because so many chronic diseases are associated with nutrient deficiencies, so many of.
These diets like you'll write a diet book for heart health. Well, it's a diet book for heart health, brain health, bone health. It's like the bottom line is these principles work across the board. Now the question is, because I know the AIP diet's a little bit more intense than say, you know, virgin diet, for example, or paleo diet is this. Then let's say that someone does the paleo diet. It doesn't take them far enough. So they do the AIP and they get, you know, they get normalized. Do they need to stay there or are they able to go back to say, typical paleo style diet?
That's a fantastic question. The answer is no, they don't need to stay there. So the AIP is designed as an elimination and challenge diet. So basically what it does is it, it tries to flood the body with nutrients at the same time as it eliminates all of those foods that do have some inflammatory compounds that may be at least contributing to driving disease activity or compounds that maybe feed the wrong kind of bacteria in the gut. And we know that our gut bacteria are really, really important for immune function. So it basically cuts out all the most likely culprits. But there's a huge sort of bio individuality effect here where people will respond differently to different foods. So part of the autoimmune protocol is this reintroduction ph where you very methodically, once every four or five days, reintroduce one food. You keep a symptom journal, right? You do it In a, in a very sort of scientific experiment type way, in order to be able to identify if that food is working for you or not. But most people are able to reintroduce a wide variety of foods. And also it's, it's incredibly empowering information because through that process you actually identify your trigger foods.
And it's so great because that is such a different conversation than having a cheat day. And that's why I love this stuff so much, is we need to connect the dots between what we're eating and how we feel and just view food as information so that we can design that diet that works for us for the long haul. It's going to be different for everybody. And then it's a different conversation. Then you don't go, oh, you know what? I'm just going to have that, you know, insert whatever it is, the cheesecake that, you know, the pizza. When you, if you knew, like how it made you feel, that it was going to make your joints ache, that was going to make something flare that you'd feel crappy for four or five days, you're not going to do it. That's why I love, I love when we pull in food journaling, which is the most powerful tool. It's like the most powerful tool free, you know, it's like such a powerful tool. And then take these foods out, let your body have its little detox and reset, and then go through one by one and see which ones work. And I'm just thrilled that we are starting to have studies on that. But I'm more thrilled that just the information's out there so that people can become empowered because there's absolutely no reason not to do this. It's like crazy not to step into this.
It also, I want to sort of emphasize that depending on a person's starting point, they can look at the lists of what to eat and what not to eat. I always try to focus on what you do get to eat because you see all these delicious foods and it doesn't feel as intimidating. But some people will look at that structure and it feels very different from where they are now. And it feels like too much. And so I think it's really important to emphasize a couple of things. You don't need to. Cold turkey, all in, right? It's not like quitting smoking. You can take baby steps towards it, right? Research it, know what the finish line is, and make iterative progress towards that. How sick you are is probably the number one factor in that decision. If you're, if you're really sick and you need that quick intervention. The motivation to go all in is a little bit higher than if you just feel crummy and you want to feel better, and then maybe it's, it's okay to take those iterative steps towards full AIP implementation. The other thing is that there's a learning curve here. But the learning curve is very much like when you first moved out of your parents home and you had to learn how to buy groceries and cook on a budget for yourself. The AIP is very much like taking that, that learning period and kind of redoing it, but it's easier the second time because you've already done it once in your life. So you're kind of, you're learning some new recipes, you're learning, you're troubleshooting your own life. So you're learning what to cook on a night where you get home from work late or you're rushed and the kids need to go to soccer and there's, there's not time. What are you going to pick up from the grocery store? That's going to be a good choice. That's within the AIP framework. You're going to figure out like, you know, what kind of things do I need to keep in my pantry, in my freezer, where am I going to get the cheapest of whatever this food is that is so important for me? And you basically have to kind of go through that learning curve again. Once you get to the other side of the learning curve, following the AIP is not hard. It just, it takes a little bit of transition time to really problem solve in. Every single person's problem solving frame is a little bit different because we all have different challenges to eating healthy and having, you know, a healthy lifestyle. So it's, there's a learning curve, but then you get to the other side and you're like, oh, look at this. You know this. Why did I ever think this was hard? This is actually really easy and look how great I feel.
And plus, you feel so much better. You know, then you have energy and focus and all that. And I just want to let everybody know that we're going to get you started, not specifically on AIP, but get you started on some of the Paleo ABCs that will include food lists and cooking tips and how to stock your pantry and all of those key things. So we'll kind of kind of slide, start sliding you in with what you're giving everybody.
It'll actually, there is some aip. There's some AIP this is like so this is great.
This is a great, easy way to start stepping into it. So you're going to be able to get this by going to jjvirgin.com paleomom and thank you so much. That is amazing what you've put together in terms of resources for everybody. Really appreciate that. Yes. And thank you for all of your awesome, awesome information. As always, I so appreciate you. Now after the break, we're going to be answering a listener's questions, so stay with us.
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Hey, welcome back. This is the time where I answer a listener's question. If you've got a question for me, I would love to answer it. So just leave it on over at JJ Virgin on Instagram or JJ Virgin Official at Facebook and I'd love to give you a little shout out and answer your question on my podcast. And of course I'm also on there live a bunch, so I'd love to meet you too. This one is from Terry who says I just got diagnosed with an autoimmune disease.
These.
Where should I start? Well, I'm going to start you on the Virgin diet. Now we have the Virgin diet and I have it done Paleo style, which is a great place to start. And you can also use a lot of the resources that Sarah is so graciously gifting us here. So I will put the link to the first part of my seven day challenge. You've also got all of Sarah's recipes, shopping lists, etc, so you've got all the information you need to get started here at jjvirgin.com paleomom. What I want you to is go through and do the Virgin Diet and the Paleo style version and do that and see how you do. Now that's set up to go through for at least three weeks as a reset and then to go back and see how you feel. But what I'd love you to do is do the first three to four weeks, get those foods out, focus paleo and then let's see how far you get. And if you have gotten to where you need to be, awesome. But if you need to go further, and this is why I wanted to bring Sarah on and have her talk about that autoimmune profile, that's the next step is to go into the autoimmune profile and to do that work. So you can start here with the elimination diet and going paleo there and then next level is if that doesn't take you as far as you need to go is to go and do the autoimmune protocol. And what I love so much that you heard today is it is amazing what you can do when you incorporate in diet and lifestyle and this is really the place you want to be. I remember when Virgin diet first came out, that's how I kind of got alerted to oh, this is a great diet to use for autoimmune is we had a gal with psoriatic arthritis who was googling anti inflammatory diet, stumbled upon it and boom, turned everything around. So again what I look at this is peeling the onion in layers. So starting there with going paleo style on the virgin diet. So you've got great resources from what everything that Sarah is giving you today. And then also you can jump into the free challenge and then if that gets you where you want to be, great. If you need to go further, the next step would go to start incorporating in the autoimmune protocol principles. And again, it is stunning what you can do with diet. And then if for some reason that doesn't get you all the way there, then you work with your doctor on what you're going to need. But I'm guessing that you can get through a lot of this and Dr. Terry Wahls is a great example of this in her TED Talk through diet and lifestyle changes. So great question. Thank you so much for asking that and I look forward to hearing how this works for you. And again, jjvirgin.com paleomom I will see you next episode. Bye.
That's all for this episode of the JJ Virgin Lifestyle show, which marks another step towards a healthier body and mind. Don't forget to rate, review and subscribe to the show and we'll talk to you next week.
Hello listeners, this is Anne Bogle, author, blogger and creator of the podcast what Should I Read next? Since 2016, I've been helping readers bring more joy and delight into their reading lives. Every week I tag all things books and reading with a guest and guide them in discovering their next read. They share three books they love, one book they don't, and what they've been reading lately, and I recommend three titles they may enjoy reading next. Guests have said our conversations are like therapy, troubleshooting issues that have plagued their reading lives for years and possibly the rest of their lives as well. And of course, recommending books that meet the moment. Whether they are looking for deep introspection to spur or encourage a life change or a frothy page turner to help them escape the stresses of work, school, everything, you'll learn something about yourself as a reader and you'll definitely walk away confident to choose your next read, with a whole list of new books and authors to try. So join us each Tuesday for what Should I Read Next? Subscribe now wherever you're listening to this podcast and Visit our website whatshouldireadnextpodcast.com to find out more.
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