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  • Writer's pictureDr Shawn M. Carney

Auto-Immune Paleo (AIP) diet: a modern elimination diet for Hashimoto's disease!

Updated: Oct 6, 2023

What happens when you combine paleo and elimination diets? A dietary plan that has shown to significantly reduce symptoms and improve quality of life for people with varying auto-immune diseases, including rheumatoid arthritis (RA), inflammatory bowel disease (IBD) and Hashimoto's Hypothyroidism.

naturopathic physician near me hypothyroidism

What is Hashimoto's disease?

Hashimoto’s disease is the most common autoimmune disorder affecting the thyroid gland and most common cause of hypothyroidism in developed countries. (1) With a 5-10 time prevalence over men, the reported prevalence in white women is in the 1-2% range among the entire population in the United States. (2) In Hashimoto's disease, immune-system antibodies lead to destruction of the thyroid's hormone-producing cells. The disease usually results in a decline in hormone production, which is called 'hypothyroidism'. Hashimoto's disease is also known as Hashimoto's thyroiditis, chronic lymphocytic thyroiditis and chronic autoimmune thyroiditis. The most common laboratory findings include an elevated thyroid-stimulating hormone (TSH), low levels of free thyroxine (FT4), and an increase in anti-thyroid peroxidase antibodies (TPO).


Paleo-Elimination Diet Fusion: 'Still like that old time rock & roll' - Bob Seger

Sorry Bob, but we are doing this paleo, without any roll!

Hashimoto's disease diet
Bob Seger - Still liking that old-time/paleo rock and roll (gluten free)

In terms of its dietary composition, AIP is a 'modification of the Paleolithic diet', and in that way, referring to it as the 'Auto-Immune Paleo (AIP) diet' seems, in my opinion, more clear.


It begins with an elimination of specific foods, dietary additives, emulsifiers, and western dietary patterns that have been implicated in disrupting the flora of the gastrointestinal microbiome, nutrient density, blood sugar balance, and immune system regulation, as well as the intestinal barrier itself. This intestinal barrier compromise, often referred to as 'leaky gut', has been shown to lead to dysregulated food particle, protein or antigen presentation and the development of autoimmunity. (6)


In addition to the eliminated foods, AIP additionally promotes the consumption of nutrient-dense whole foods and strategic meal planning. Encouraged foods include vegetables, fruits, mono- and polyunsaturated fatty acids, tubers, wild game, poultry, organ meats, and non-processed meats. In general, it is suggested to eat plenty of fermented foods to support healthy gut flora, unless someone has histamine intolerance or small intestinal bacterial overgrowth (SIBO). Also, making sure people don’t allow themselves to get too hungry or hypoglycemic by including sufficient appropriate fats and protein in the diet is advised, as is eating frequently enough to avoid energy crashes caused by low blood sugar.


A Closer Look at AIP diet

On the AIP diet, you remove all grains, legumes, nightshades (such as eggplant and peppers), dairy, eggs, coffee, alcohol, sugar, oil and food additives from your diet. After a 1-3 months, you can work the excluded foods back in one at a time to figure out which foods trigger an inflammatory reaction. This process can help you reduce inflammation throughout your body.


Foods to eat on the AIP diet:

  • Most organic vegetables: Include as much variety as possible, making sure to include the full color spectrum. Avoid nightshades.

  • Meats, as organic as possible, even organ meats: Select hormone-free, antibiotic-free, and pastured meats.

  • Fish and shellfish: Seek out ocean-caught cold water, low-mercury fish with high fat content.

  • Quality fats: Choose pasture-raised, grass-fed animal fats, fatty cold water fish, olive oil, avocado oil, coconut oil, and low-mercury Omega 3 supplements.

  • Low glycemic organic fruits: Eat fruits lower in sugar and eat them with fat, fiber, or protein to slow the uptake of sugar.

  • Probiotic and fermented foods: Fermented foods include sauerkraut, kimchi, fermented pickles (not packed in vinegar), coconut yogurt, kombucha, water-based kefir.

  • Coconut: Enjoy coconut and coconut products that are free of sugars or additives.

  • Herbs and spices: Avoid nightshade herbs such as peppers during the elimination period. Good options include basil, cilantro, cinnamon, clove, garlic, ginger, horseradish, lemongrass, mace, mint, oregano, parsley, rosemary, sage, saffron, sea salt, thyme, turmeric.

  • Vinegars: Avoid grain-based vinegars and instead choose apple cider, balsamic, champagne, coconut, red wine, sherry, ume plum, or white wine vinegars.


Foods to avoid on the AIP diet:

  • Grains

  • Beans and legumes: This includes products made from peanuts and soy, which are legumes.

  • Nuts

  • Seeds

  • Seed-based spices: These include anise, annatto, celery seed, coriander, cumin, fennel, fenugreek, mustard, nutmeg, poppy seed, sesame, allspice, star anise, caraway, cardamom, juniper, peppercorns, sumac, whole vanilla bean.

  • Dairy: This includes dairy from sheep or goats and raw dairy.

  • Eggs

  • Nightshades: Nightshade vegetables include eggplant, goji berries, sweet and hot peppers, hot pepper sauces, tomatillos, tomatoes, and white potatoes.

  • Nightshade-based spices: These include cayenne, chili powder, paprika, red pepper, and curry.

  • Refined and processed oils and vegetable oils

  • Sugars and sweeteners, including natural ones

  • Artificial sweeteners

  • Emulsifiers, thickeners, and other food additives: Watch out for guar gum, carrageenan, xanthan gum, cellulose gum, soy lecithin, and other additives.

  • Alcohol

  • Hidden sources of gluten: Always read the labels as gluten is hidden in many foods and additives. Beware of non-specific ingredients such as “natural flavorings.”


So if seeking assistance with managing auto-immune conditions and/or Hashimoto's disease, contact our clinic using the information above. And consider subscribing to our newsletter, visiting our dedicated landing page for hypothyroidism and Hashimoto's or seeing other related blogs.









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The content and any recommendations in this article are for informational purposes only. They are not intended to replace the advice of the reader's own licensed healthcare professional or physician and are not intended to be taken as direct diagnostic or treatment directives. Any treatments described in this article may have known and unknown side effects and/or health hazards. Each reader is solely responsible for his or her own healthcare choices and decisions. The author advises the reader to discuss these ideas with a licensed naturopathic physician.



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