11 Diets for Addressing Chronic Health Conditions

Adapted from episode 39 of my podcast, The Perfect Stool: Understanding and Healing the Gut Microbiome.

There are tons of special diets meant to help reveal food sensitivities, address physiological imbalances or reverse autoimmune disease or other chronic conditions. I’ll cover 11 of them in this article. This may give you a starting point for trying a more targeted elimination or other special diet. Or if you’ve already done the elimination diet thing with no luck, even one as strict as the paleo autoimmune protocol or AIP and it didn’t help you, this may give you some completely new ideas, because there are many diets for different health issues that are not a subset of the AIP.

Gluten-free Diet

So let’s start with the most basic: gluten-free. Gluten is commonly known as the protein found in wheat of all kinds, including einkorn, durum, khamut and semolina, as well as barley, spelt, triticale and rye and frequently oats because of cross-contamination. However, gliadin is actually the subfraction of gluten that’s found in the grains I just mentioned and that has received the most attention. And it’s hidden in tons of foods, like soy sauce, soups, salad dressings and spices, so you’ll need to find a thorough list of potential sources and stay away from processed foods with questionable ingredients while you try it. This is step 0 for anyone with gut or autoimmune issues of any type. I did a whole podcast episode on this (episode 21) if you want more detail. However, before you give up gluten, please go to your doctor’s and get tested for celiac disease, which is an inflammatory condition of the small intestine. If you do a lot better on a gluten-free diet and you haven’t been tested, the only way to get tested is to start eating gluten again, and if you’re feeling much better, you won’t want to do that. But having that celiac diagnosis will make you take the diet a lot more seriously and requires a much higher level of vigilance, like separate cutting boards and removing personal care products with gluten in them. Of course, you may not have celiac but could have non celiac gluten sensitivity (NCGS), which you’ll find out by giving up gluten and seeing how you do. If you are gluten sensitive and you just ignore it and eat gluten, you can end up with autoimmune disease, osteoporosis, asthma, mental health issues, fibromyalgia or chronic fatigue.

Another big subset of people that the evidence shows should try a gluten-free diet are those who have already been diagnosed with an autoimmune disease, especially Hashimoto’s thyroiditis (the most common cause of hypothyroidism) and Grave’s disease. This is because the protein in gluten looks a lot like your thyroid cells. This type of autoimmune disease is believed to start when you have a leaky gut (which may be because of the gluten or for some other reason like a gut infection) and the undigested gluten proteins escape into your body, creating an immune attack to remove these proteins. Then because of molecular mimicry, or the resemblance of gluten and thyroid cells, your body attacks your thyroid. But really experts recommend cutting out gluten for any type of autoimmunity.

So I’m not going to lie: cutting out gluten is tough and may seem impossible, but I’ve gone mostly gluten-free for about 7 years now because I was diagnosed with Hashimoto’s thyroidits, and honestly it’s a relief, mainly because it keeps me from eating things that make me feel bloated and terrible like bread and pasta, and encourages me to eat more nutrient-rich foods. And it keeps me from indulging in so many unhealthy, sugary things that have gluten in them. Although I have to admit that I do cheat about 6 times a year, eat pizza and take enzymes to digest it now that my Hashimoto’s antibodies are down to normal levels.

But when first faced with the prospect of going gluten-free, you might be thinking: what about a chewy delicious pizza crust, or a sandwich on beautiful toasted ciabatta bread, or your favorite bowl of pasta? Fortunately, there are lots of great alternatives to those foods now and gluten-free bakeries in most cities. Although, I’ve always been of a mind that you’re better off looking for recipes that are naturally gluten-free, like with a lot of Asian recipes that are naturally gluten-free (provided you use tamari or gluten-free soy sauce instead of soy sauce).

But if you’re looking for good alternative flour options, two of my favorite low-cost and neutral-tasting, grain-based ones for baking are sweet sorghum and millet (which I combine, and then you need to add a starch like cornstarch or tapioca starch as 1/3 of the mix). I don’t add binders like xantham gum to my gluten-free flours. Rather, I look at any individual recipe to see if that addition is necessary and try to use more natural binders like flax or chia seeds, ground up and mixed with water.

My favorite grain-free flours are almond and cassava flours, and then I use tapioca starch (or arrowroot starch) as my starch, which is just the starch from cassava flour, but it’s much less expensive than whole cassava flour. And there are tons more grain and grain-free options including: amaranth, arrowroot, buckwheat, millet, cornmeal, flax, chia, coconut, oat, quinoa, rice, mesquite, bean flours (garbanzo, fava, etc.), tigernut and many more. And if you’re looking for amazing angel hair pasta that’s gluten-free (and very hard to find), I love the BGreen Millet Angel Hair*.

One caution about going gluten-free is not to just switch to gluten-free junk foods with additives and fillers (and often a lot of sugar), or based mostly on rice flour. They have found elevated levels of arsenic in people eating gluten-free because of high rice consumption so think more about following a whole foods diet minus gluten that includes other sources of starch, like root vegetables, nuts and other grains besides rice.  

A final note that while it’s well-known that gluten causes celiac, it’s less-known that gluten can cause inflammation in other parts of the body including the mouth, esophagus, stomach and small and large intestines. I had one client who came to me for weight loss who was also hypothyroid. I had her do an elimination diet including gluten. Wouldn’t you know, after she had been working with me for about 4 months, she saw her dentist, and all of 4’s and 5’s with the depth probe were now healthy 3’s. So she had all this inflammation going on in her body that wasn’t super obvious but cleared up after eliminating gluten. So given gluten is connected to inflammation, and inflammation to most chronic diseases, eliminating gluten is a viable option to address many different conditions, not just celiac.

Grain-free Diet

So if you start with gluten and that doesn’t seem to be enough, you may want to go the whole way to grain-free. More restrictive than the gluten-free diet, the grain-free diet(as the name suggests) involves cutting out all grains, which technically are the seeds of grasses. The reason to try this is because you may not just be sensitive to gliadin but to other prolamines found in other grains traditionally considered gluten-free, like corn, rice, millet, oats, wild rice, fonio, job’s tears, sorghum, millet and teff. So if you find that you’re 75% better off without gluten but not all the way, you may be sensitive to all prolamines in grains and should give a grain-free diet a try.

Anti-inflammatory diet

So the next diet I wanted to cover is an anti-inflammatory diet. Reducing inflammation, as I’ve mentioned, can be a powerful way to reduce your risk of illness and reverse a chronic illness you already have. Chronic inflammation is linked in research to heart disease, arthritis, cancer, diabetes, depression and Alzheimer’s. Since I’ve heard the term anti-inflammatory diet floating around on the internet quite a bit, I wanted to include what that was, but quickly realized that there is no set definition of an anti-inflammatory diet. Pretty much everyone agrees that it eliminates added sugars, deep fried foods, partially hydrogenated oils (which are mostly out of the food supply thanks to the Obama administration, as long as a serving has less than ½ a gram, which will be labeled as 0 grams), ultra-processed foods, and refined carbohydrates like white bread, pasta and desserts. Then depending on who you’re talking to, it may reduce or exclude red meat, saturated fat, processed meats, gluten, dairy, soy and/or processed seed oils. And then also important is what you do focus on, which is getting lots of servings (think 5-9) of fruits and vegetables/day, with a particular focus on green leafy vegetables, cruciferous vegetables like broccoli, cauliflower, cabbage and Brussels Sprouts; alliums like garlic, onions, scallions and leeks, fats like olive oil and avocado oil, nuts, fatty fish and seafood with lots of omega 3 fatty acids (like sardines, anchovies, salmon or tuna, but be sure to choose only brands of canned tuna that boast low mercury like Vital Choice* or Safe Catch*) and anti-inflammatory spices like turmeric, ginger, cloves, rosemary and thyme. And of course you should choose organic and/or pasture-raised foods and for meats, dairy and eggs. And then it’s also important on an anti-inflammatory diet to get lots of fiber, so that can come from fruits and veggies, or whole grains if you’re eating grains, or nuts, for example. Or dark chocolate – that’s one of my favorite sources of fiber.

Basic Elimination Diet

Next item up, the basic elimination diet. So for my clients, if they are having digestive issues and haven’t already done it, I often suggest a basic elimination diet. Because if you’re showing signs of leaky gut, like migraines, brain fog, joint pain, or skin issues, not to mention GI issues, it is often a combination of foods, not just one food like gluten, that’s causing you to react. Eliminating only gluten or only dairy or just those two and not feeling better could leave you with the false conclusion that those foods are fine for you, when in fact the issue is that you are sensitive to several foods.

So generally, I suggest a whole-foods elimination diet for at least a month that excludes gluten, added sugar, dairy, soy, caffeine, alcohol, processed foods and seed oils. Then each item (except crappy processed foods and seed oils, which you shouldn’t reintroduce at all, and the sugar, which should remain limited) should be reintroduced alone for a couple of days Eating the reintroduced item at least 2 servings a day until you feel a bad reaction, or if not, wait a couple days after that for any delayed reaction. Now of course if this isn’t enough for your symptoms to improve, you can start excluding additional foods, like nightshades, nuts or legumes, or go for a full autoimmune protocol, which I’ll get to later. I think this kind of elimination diet is a good start for people who aren’t prepared to try something as extreme as the autoimmune protocol or AIP. I know that when I found out I had Hashimoto’s thyroiditis and saw the AIP, I was like, “No way!” It was just a nonstarter for me because it felt like there would be nothing left for me to eat. But when I tried this pared-down elimination diet, my symptoms improved and I was able to isolate gluten, dairy and soy as the most problematic foods for me. So if you have an autoimmune disease that isn’t profoundly impacting your health yet, this may be a good start.


If you haven’t been living under a rock, you’ve likely heard of the paleo diet, which was developed by Robb Wolf. Formerly a research biochemist, Wolf is the bestselling author of The Paleo Solution: The Original Human Diet* and Wired to Eat*. And along with the paleo diet is a whole school of thought known as ancestral health, approaching lifestyle and nutrition from the perspective of our hunting and gathering ancestors, who if you pull out high rates of infant mortality, lived long and healthy lives. And spent a heck of a lot less time working that we do to maintain it. So generally, you can pretty much figure out the foods that would have been accessible to hunter gatherers: meats, animal fats, coconut oil, seafood, root vegetables, other fruits and vegetables in season, nuts and seeds and natural sweeteners like maple syrup and honey in limited quantities.

Processed foods of any kind are out, unless of course they’re made to be paleo, as is alcohol, all dairy except clarified butter or ghee, all grains, starchy vegetables like potatoes, corn and peas, factory farmed meats, beans and legumes, including peanuts and soy, refined or processed sweeteners and processed seed oils. One of the biggest brands of paleo products is Primal Kitchen, which makes very nice dressings* made from avocado oil and now has frozen entrée options for people who don’t cook. I aspire to the paleo diet, except I’m too weak to eliminate all grains when my family eats them in front of me, and fakish foods like sugar alcohols because at the end of the day I have found that added sugar in any form, even if it’s ancestrally okay, causes me to gain weight. Not to mention alcohol, and legumes, which I believe are healthy, high-fiber foods for most people.

On the Paleo diet, ideally you should be eating a wide variety of proteins from as many animal sources as possible. This means not relying on standard cuts of meat and lean meats, but including the fatty meats and organ meats, not shying away from saturated fat in meat or coconut oil, and including bone broth and other good collagen sources. If you’re a baker, paleo baked goods typically use cassava flour or coconut flour, as well as arrowroot or tapioca starch or other non-grain flours. In addition to meat, vegetables, nuts and seeds, avocados, olive oil and fish oil are staples in a Paleo diet. And root vegetables, including sweet potatoes and winter squash, are the primary sources of starches. The paleo diet has been shown to be anti-inflammatory, promote weight loss, reduce digestive issues, and reverse or decrease the likelihood of developing chronic diseases.

Paleo Autoimmune Protocol (AIP)

Next up, AIP or the Paleo Autoimmune Protocol. So if you’re tried the paleo diet and feel better but not all the way better, you may want to implement the AIP, which includes an elimination diet designed to reverse autoimmune disease by addressing the nutritional resources required for immune regulation and tissue repair as well as removing inflammatory factors from your diet. The protocol also focuses on your lifestyle. So what’s involved in AIP? The AIP addresses four areas known to contribute to autoimmune diseases, which are: nutrient density, gut health, hormone regulation and immune system regulation. Meat, seafood, copious amounts of vegetables, fruit and healthy fats are AIP-approved. You might be thinking: isn’t that the same as the Paleo diet? It’s sort of like the paleo diet on steroids and further eliminates eggs, nightshades (which include potatoes, tomatoes, peppers, chilies, eggplant, tomatillo, goji berries and ashwagandha), seeds, nuts, ghee, chocolate, caffeine and seed-derived and nightshade-based spices.

The AIP diet has been attributed to Dr. Loren Cordain, PhD, a scientist responsible for discovering that certain foods trigger inflammation in people with autoimmune disease. Other leading experts in the AIP field are Robb Wolf, for his contributions in The Paleo Solution, and Dr. Sarah Ballantyne, PhD, who researches and writes extensively on autoimmunity and diet. Her research-heavy tome on autoimmune disease is called The Paleo Approach*. The main thing to remember about AIP is that it’s an elimination diet, which involves the removal and systematic reintroduction of potential problem foods, but that it is meant to last a lot longer than a typical elimination diet – pretty much as long as it takes for gut inflammation to settle down. I would generally consider recommending it for someone with an autoimmune disease that involves bad joint pain or other significant pain or disability or potential for future problems, along with gut testing and healing of gut infections that could be at the root of food sensitivities.

Low-Oxalate Diet

The next diet I’m going to talk about is the Low-Oxalate Diet. So if you’ve been rattling around the world of functional medicine for any length of time, you may have heard about oxalates. You probably even know they’re in spinach. What I’ve discovered since I’ve started using the Organic Acids Tests to uncover gut and other health issues, is that pretty much any client who has a high level of yeast metabolites also has a high level of one of three markers of high oxalates, because oxalates are produced by yeast. Oxalates are crystals that can cause kidney stones, most of which are made of calcium oxalate, but are also less known for their role in fibromyalgia, vulvodynia or vulvar pain, autism, anemia, urinary tract infections, interstitial cystitis and crystal formation in other places like bones, joints, blood vessels, lungs, thyroid and even the brain. Wherever they’re found, oxalate crystals can cause pain and damage and increase inflammation.

The first thing to know about starting a Low-Oxalate Diet is that you should reduce your oxalate intake slowly. So for example if you’re eating over 500 mg of oxalate each day, you should be reducing at a rate of no more than 5 percent per week. Basically that means reducing about 25 mg each week. If you’re eating 500 mg or less of oxalates, you can come down 10 percent each week. This is to avoid a phenomenon called oxalate dumping, which is a horrifying thing where oxalate crystals start coming out of your body wherever they are present. So you might be asking at this point, what foods are high in oxalate and how would I even know if I have an oxalate toxicity issue?

Foods that are high in oxalates include:

  • beer
  • beets
  • beans
  • berries
  • coffee
  • dark green vegetables
  • nuts
  • oranges
  • spinach
  • soy milk
  • soda
  • tofu
  • wheat bran
  • sweet potatoes
  • black tea
  • rhubarb

This might seem like a random list, but if you’ve noticed difficulty with some of these foods in the past (or perhaps all of them), or you have any of the conditions I mentioned before, it’s possible you have an oxalate toxicity issue. If you suspect oxalate toxicity might be your issue, or you just want to learn more about the Low-Oxalate diet and what’s involved, there’s a great website with recipes and a chart of oxalates in various foods from actual studies measuring oxalates in these foods. They also have a Facebook group called TryingLow Oxalates. Also, one way you can help remove oxalates from your body or diet is by eating a full serving of dairy or a calcium citrate supplement* with meals, which will absorb and usher oxalates out in your urine.

Low-Histamine Diet

Next up is the Low-Histamine Diet. If you have allergies, I’m sure you’ve heard of “anti-histamines,” which are drugs like Claritin, Benadryl and Zyrtec that treat allergic rhinitis and other allergies. But what is histamine? A histamine is a compound released by your MAST cells that plays a part in your body’s immune and inflammatory responses. So when your immune system is triggered by a potential threat, histamine is released through your bloodstream. Then your blood vessels dilate and this creates an inflammatory response with common allergy symptoms like sniffling, sneezing, coughing, tearing up or itching. Histamine intolerance occurs when high levels of histamine are chronically built up in your body. Common symptoms of histamine intolerance include irritability, depression, brain fog, dizziness, rash, flushing, hives, headache, tissue swelling, altered bowel function, nausea, vomiting, abdominal cramps, non-celiac gluten sensitivity, runny nose, difficulty breathing and insomnia.

There are two reasons why histamine can become chronically elevated: either there’s something producing high histamine levels in your body or an inability to clear histamine from your body. So what causes high histamine levels? It could be allergies (as I mentioned), but it could be other things too, for instance gut dysbiosis, environmental mold exposure, a leaky gut, GI bleeding, alcohol, genetics and histamine-rich foods. Foods high in histamine or that cause a release of histamine include:

  • avocados
  • eggplant
  • tomatoes
  • sauerkraut
  • papaya
  • pineapple
  • dried fruit
  • strawberries
  • citrus
  • all nuts and peanuts
  • fermented dairy products like yogurt and kefir
  • coconut yogurt
  • aged cheese
  • cured or old meats
  • shellfish
  • smoked fish
  • soy sauce
  • miso
  • mayo
  • pickles and olives
  • sauerkraut
  • kimchi
  • relish
  • soy sauce/tamari
  • chickpeas
  • soybeans
  • aged cheeses
  • chocolate
  • alcohol
  • energy drinks
  • black and green tea

Leftovers are also high in histamines, which build up the longer food ages.

Low-histamine foods include:

  • herbal teas
  • leafy herbs
  • coconut oil
  • olive oil
  • freshly cooked meat
  • poultry (frozen or fresh)
  • eggs
  • coconut milk
  • rice milk
  • hemp milk
  • almond milk
  • gluten-free grains
  • fresh fruit
  • most vegetables

If a Low-Histamine Diet works for you, then you will probably want to figure out whether there’s a root cause you haven’t addressed, or if you have something called Mast Cell Activation Syndrome, which includes not just a release of histamine but also other inflammatory mediators, of which histamine is one.

Low-Sulfite Diet

The next diet is a Low-Sulfite Diet. One more potential allergen that could be causing your problems are sulfites. Symptoms of a sulfite allergy are typical allergy symptoms, including hives, itching, trouble breathing or swallowing, GI symptoms like an upset stomach, diarrhea and vomiting, flushing, dizziness and a drop in blood pressure. Sulfites are preservatives widely used in the food industry to prevent discoloration and browning of processed foods. Depending on the manufacturer, foods that may (or may not) contain large quantities of sulfites are:

  • molasses
  • jams and jellies
  • tomato paste
  • corn starch
  • potato starch
  • guacamole
  • gelatin
  • fruit and vegetable juices
  • fish
  • crustaceans and shellfish
  • dried fruits and vegetables
  • lunch and processed meats
  • condiments
  • canned and frozen fruits and vegetables
  • bottled lemon and lime juices and concentrates,
  • alcoholic and nonalcoholic cider
  • wine and sparkling wine
  • vinegar

Look for a sulfite-free label to be sure. Sulfites can also be found in medications and personal care products. So if that group of foods speaks to you, you may want to look into a Low-Sulfite Diet.

Low-Salicylate Diet

Next up is a Low-Salicylate Diet. Another potential source of dietary sensitivities may be coming from salicylates. A big tip off to this would be a sensitivity to aspirin or other non-steroidal anti-inflammatory drugs. Reactions can range from the urinary/gastrointestinal, like diarrhea, urgency or stomach pain, to fatigue, to the mental, including depression, memory loss, hyperactivity or trouble concentrating, to typical allergy symptoms like burning or itchy eyes, trouble breathing, tinnitus, headaches, rashes, rhinitis and swelling of hands, feet, eyelids, lips or face.

If you’re sensitive to salicylates, foods you’ll want to try reducing or eliminating include:

  • tangerines
  • pineapples
  • oranges
  • most berries
  • herbs and spices (including cinnamon, rosemary, thyme, oregano, turmeric and mint)
  • nectarines
  • green apples
  • black tea
  • asparagus
  • all dried fruits
  • fruit juices

You also will want to avoid topical and inhaled exposure, because salicylic acid is easily absorbed through the skin and lungs. Many household items and toiletries typically contain substantial amounts of salicylates or salicylic acid, including: wart and callus removers, topical creams, toothpaste, soaps and cleansers, shaving cream, shampoos and conditioners, muscle-pain creams, mouthwash, lozenges, hair products, fragrances, detergents, cosmetics, cleaning products, chewing gum, bubble baths, breath mints, Alka-Seltzer, air fresheners, acne products, drugs for IBD and supplements containing willow tree bark extract.

Low-Sulfur Diet (for CBS Mutation/Sulfation Issues or Hydrogren Sulfide SIBO)

The last diet I wanted to cover was a Low-Sulfur Diet, which is indicated for someone with what’s called a CBS mutation, which causes issues with sulfation (one of the essential processes for detoxification,  also involved in hormone regulation, cell signaling and molecular recognition). When you eat sulfur compounds, your body produces ammonia as a byproduct, which is toxic, but is usually eliminated through the urine. If you have a CBS mutation that’s high firing, you may end up with excess ammonia, which can cause symptoms like lethargy, fatigue, shortness of breath, tremors, seizures, poor coordination, lack of muscle control, visual disturbances, headaches and nausea. In addition, you could have an overgrowth of microbes that produce ammonia as a byproduct that’s exacerbating your condition. I had a client who had these kind of symptoms every time he ate sugar or carbs and had to go to the urgent care for a three-drug cocktail just to handle it. When we did his Organic Acids Test and I saw his orotate level was elevated, in conjunction with these symptoms, I suspected a CBS mutation. Sure enough, he did a 23andme and confirmed that he did have the mutation. Educating him about supplements to reduce ammonia-producing microbes (including candida) in his gut has greatly improved his condition, as has strategically using certain amino acids. For people with this mutation, Dr. Jockers recommends a diet consisting of 70% fat, 10-20% carbohydrate and 10-15% protein or under 50 grams/day and limiting sulfur intake by removing garlic, onions, cruciferous veggies, eggs, legumes and all protein-rich dairy. And it’s also recommended that you add in one root vegetable, particularly known for removing ammonia, which is yucca, also known as cassava. It’s actually used in aquaculture to control ammonia levels and fed as a supplement to fish and shrimp. Also, in my client’s experience, removing sugar and carbs was a really essential component to feeling better because candida feed on sugar and carbs and were adding to his ammonia load as a byproduct of their metabolism. Lucy Mailing, PhD also recommends a similar diet for people diagnosed with an overgrowth of hydrogen sulfide producing bacteria. Your tip-off that this may be an issue is when your gas smells like rotten eggs. Her recommendations include a diet void of animal foods and dairy for 3-4 weeks, low fat, only olive, avocado and coconut oils, and avoiding sulfur-containing vegetables if they cause symptoms.

So that’s a lot of information, I know, but hopefully it may have given you a place to start on understanding the variety of potential diets that can be used to address gut and health issues.

When I’m working with clients, I help them understand what dietary protocol might be best to try, along with simultaneously testing the gut through the GI Map or Organic Acids Test to see if there is another root cause of their symptoms.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Schedule a Breakthrough Session Now

Listen to episode 39 of The Perfect Stool: Understanding and Healing the Gut Microbiome.

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