Six Principles to Follow When Starting on an Autoimmune Diet


Inspired by a combination of his work treating patients with autoimmune disease and working in his garden, Dr. Cowan has developed six principles to help patients create healthy, natural diets. He emphasizes the importance of sourcing quality food from your immediate environment and consuming the correct macronutrients.

The following excerpt is from Vaccines, Autoimmunity, and the Changing Nature of Childhood Illness, by Thomas Cowan, MD. It has been adapted for the web.

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Listen to the following excerpt from the audiobook of Vaccines, Autoimmunity, and the Changing Nature of Childhood Illness.

The Cowan Autoimmune Diet

The Cowan Autoimmune Diet is based on the etiology of autoimmune disease as I describe it in this book. For example, one of the first steps in the progression of any autoimmune disease is disturbance in the gut microbiome; this can be addressed through a proper diet. Another factor is deterioration of the intestinal villi; this can also be addressed through a proper diet. The principles in the Cowan Autoimmune Diet are by no means unique; they can be found in the GAPS diet, the Autoimmune Paleo Diet, and the Wahls Protocol. These are all wonderful dietary approaches and I have used each of them successfully in my many years of treating people with autoimmune diseases.

I have a slightly different take than these other approaches, which I’ve developed in my role not only as a physician treating patients with autoimmune diseases but also as a gardener.  The other perspective I bring comes from my emphasis on water. Water molecules make up more than 99.9 percent of the molecules in our bodies. And the state of our health is in many ways a result of how well we are able to structure this water in our cells and tissues. Finally, while the thrust of this book is on the understanding and treatment of autoimmune diseases, and this diet is considered a part of that therapy, we must never lose sight of the importance of finding joy in our lives.

Food is an integral part, in every culture and society, in the attainment of this joy. The sensual quality of food, including not just its taste, but its aroma and appearance, is an essential part of this diet and an essential part of any true healing. Our quest should be for a life of abundance, joy, and meaning. There is no greater venue for executing this quest than in our relationship with food. With that introduction, here are the principles of the Cowan Autoimmune Diet.

Food Quality

In some ways, in a list of the top ten dietary principles, attention to food quality should be numbers one through nine. As there is such an intimate connection between pesticide or herbicide use and diseases, including polio and autism, it is imperative for anyone suffering from any autoimmune disease, or any disease of any kind, to pay strict attention to the quality of food they’re eating. By “quality,” I refer not only to the care of soil and pastures that forms the foundation of healthy food, but also to more subtle aspects, such as the correct time to harvest vegetables and the proper way to store and process the foods we eat.

roots A commitment to food quality needs to be a total commitment—meaning the complete abandonment of inferior-quality foods. Here are the “rules”:

  • The best food is properly foraged or caught wild. This means the forager or hunter needs to be aware of sustainable foraging practices and must avoid contaminated land and water. The hunter needs to be aware of how to humanely kill and dress his prey. The next-best quality will come from pastured animals, followed by food grown on biodynamic farms or gardens or on small-scale permaculture farms. Following that is food produced by small-scale family farms or gardens or food grown in your own organic homestead or garden. The final acceptable source is food grown on large-scale certified organic farms. For help finding these types of foods, the Weston A. Price Foundation shopping guide can be invaluable (see recommended resources).
  • Processing should either be not at all or by traditional techniques that have stood the test of time. Foods that undergo no processing include fresh salad or cucumbers right from the garden or farmer’s market. Examples of traditional processing techniques, which in many cases enhance the quality of the food, include traditional lacto-fermentation; making butter or fermented dairy products (e.g., kefir, yogurt) from pastured, 100 percent grass-fed whole milk; or the production of traditionally cured meat products such as bacon or prosciutto. Other quality-enhancing processing techniques include making sourdough bread from freshly ground heirloom grains, soaking or sprouting of seeds and nuts, and making lacto-fermented drinks from excess garden produce. These and many more techniques for enhancing food quality can be found in the book Nourishing Traditions, by Sally Fallon Morell and Mary G. Enig.
  • Finally, and especially relevant to those who have their own gardens, leaf and fruit vegetables such as kale, lettuce, zucchini, and peppers should be harvested as early in the morning as possible, whereas root vegetables such as carrots, beets, parsnips, and horseradish are best harvested in the evening. While this may seem like a small point, the energy of the plant is most concentrated in the leaves early in the morning, enhancing the flavor and allowing them to be stored longer in the refrigerator. On the other hand, through the day the energy and nutrient flow of the plant drops down into the roots, so root vegetables will store and retain their freshness longer when harvested in the evening.

Macronutrient Content

Dietary macronutrient content refers to the proportion of fats, proteins, and carbohydrates. The optimal relationship of macronutrients in our diet can be loosely described as liberal good fats, modest protein, and low carbohydrate. While I hesitate to give numbers, the best guide is that each meal should contain a sufficient amount of fats. The four main fats to use are grass-fed butter, grass-fed ghee, coconut oil, and olive oil. Other fats and oils that can be included (provided they are the best quality) include lard from pastured pigs, beef tallow, and duck fat. With other plant oils, we run into the problem of extraction and production of most seed and flower oils; most seeds and flowers typically need high-temperature grinding in order to extract the oils. This high-heat process harms the oils and decreases the nutrient content. The only acceptable quality source I know for true low-heat oil extraction, followed by the preservation of the oil in Miron jars, is a company called Andreas Seed Oils (see recommended resources).

mealProtein generally comes from a modest serving at each meal of animal products, which can include fish, meat, eggs, whole-milk raw cheeses, or organ meats. By “modest,” I mean about the size of a deck of cards; more than that is unnecessary and can create an undue burden on the kidneys. In addition to this portion of protein at each meal, soup or bone broth from any quality animal source should also be included. Everyone should eat at least one cup of gelatin-containing broth each day; those with an autoimmune disease should eat one cup up to three times a day. The gelatin proteins in bone broth are key for healing and sealing the gut and are therefore at the core of my autoimmune treatment program. All broth should come from the bones of 100 percent grass-fed, pastured animals in order to avoid contamination from chemicals such as glyphosate that are found in all commercial animal feed. There are almost no exceptions to this.

Finally, carbohydrate content should be low. This is the only time I give people a specific number: generally between 45 and 75 grams of net carbohydrates per day. There are many good books, particularly those that advocate very low carbohydrate or ketogenic diets, that can guide you in how to count carbohydrate grams in your diet. Fats are a more efficient fuel for our bodies than carbohydrates are, and our true need for dietary carbohydrates is small. As advocated for in the GAPS diet, most people with an active autoimmune disease should go six months without any disaccharides, which means the elimination of all grains and beans.

Lacto-Fermented Foods

When signs of trouble, such as autoimmune symptoms emerge, we must redouble our efforts to introduce beneficial microbes into our GI tract. We can play in soil, gardens, and compost, particularly with our bare hands, and eat an abundant supply of as great a diversity of microbes as possible. We can do this by bringing the art of fermentation back into our homes. Many wonderful books have been written about how to ferment foods, but none are better than The Art of Fermentation, by Sandor Katz. Daily consumption of as wide a variety of lacto-fermented foods, preferably home or locally made, is key in the restoration of health. Start with fermented vegetables such as sauerkraut, beet kvass, and kimchi, and then move to homemade cultured dairy products, fruits, and other beverages. For those with the inclination, even the traditional fermentation of meat and other animal products will increase the diversity in your diet and microbial consumption. Eat at least a small amount of fermented vegetables or drinks with each meal and, depending on your tolerance, increase consumption of traditional lacto-fermented foods to about 10 percent of your daily diet. Over time, just this change is an effective step in the restoration of a healthy, diverse microbiome.


Exposure to as wide a variety of foods as possible is the key to ensuring that you will consume all the vitamins, minerals, phytonutrients, and other disease-prevention agents you need that the plant and animal world makes available to us. I have been trying to incorporate this principle in my life for decades, to the point of counting precisely how many different plants I eat in a month. The key to this is to eat seasonally, grow your own garden, include perennials, and use herbs and spices liberally in cooking. Everyone should spend a month keeping track of their personal diversity consumption; aim for between twelve and fifteen different plants each day and between sixty and eighty each month. Eat widely from all the healthy animal products available in your area. Connect with a hunter in your area to have access to otherwise unavailable wild game and other hard-to-obtain animal products. Be creative and learn to use wild foods in flavorful dishes. In so doing you reaffirm your connection to the world of nature around you.


I put a lot of emphasis on the quality of water in our cells, tissues, and bodily fluids such as blood, lymph, and cerebrospinal fluid. The quality of the water in our bodies is related to the quality of water we consume in our food and drinks. The best water is highly mineralized, highly structured at a temperature of around 4° Celsius, which is generally only attainable from glacier runoff in the few remaining pristine places on earth. So, knowing that the perfect solution to water consumption doesn’t exist, we need to try and obtain the best possible water for our bodies.

waterWhen you choose a water source, the water should contain as few contaminants as possible. This includes everything from the fluoride and chlorine/chloramines put in most municipal water supplies, to such things as pharmaceutical drugs and agricultural chemicals. Besides getting the “stuff ” out of the water, healthy water should be in motion, particularly in a spiral motion. Water in a spiral motion, as it often exists in nature, is energized and structured. In plant experiments, it’s been shown that watering plants with structured, vortexed water increases the vigor and health of the plants. I have frequently been impressed when observing positive health effects in my patients who commit to consuming only structured water.

Trust Your Instincts

The final principle of the Cowan Autoimmune Diet is for you to use yourself as the most important feedback device in determining which foods work best for you. Understanding the effects foods have on you is a skill that improves with practice and commitment. The commitment here is to pay attention and honor your instincts. If you have any sense that a certain food doesn’t agree with you, skip it for at least a week, then try it again and pay close attention to how you feel after eating it. Gradually your instincts will sharpen and become clearer, but only if you make an absolute commitment to pay attention and honor your inner voice that informs how you react and feel related to your food intake. Sharpening of instincts happens to everyone who makes an absolute commitment to eating real foods; with this commitment you will be well on your way to having a unique diet, designed for you, by you, that works for you. Commitment is the holy grail of dietary therapy.

To summarize, these six dietary principles should get you off to a good start in organizing your autoimmune diet. For the first six months omit all grains, beans, and noncultured dairy products, which can then slowly be reintroduced. Be creative in the procurement, processing, and final preparation of your foods. Enjoy your meals, make mealtime a family and connection time, and consult the various books on traditional foods that I recommend for further ideas on the organization of your daily diet.

Recommended Reads

Foods for a Healthy Bacterial Flora

Making Delicious Recipes on a Restrictive Diet —With Love!

Read The Book

Vaccines, Autoimmunity, and the Changing Nature of Childhood Illness


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