AdobeStock 107422791 1

The Diet Matrix

Joy Cutrone, Wellness & Certified AIP Coach, FMCHC-Candidate
intro e1516509164739

Reduce inflammation, increase nutrient density

This isn’t about weight loss (although right-sizing* is typically an outcome of a non-inflammatory diet). This is about reducing and preventing inflammation, deepening and broadening your nutrient intake, and providing wildly soul-nourishing foods so that you don’t feel deprived when you transition from your eating norm.

Finding the right diet for you is the single most important factor in the multi-factorial approach to healing autoimmunity. The gold standard for doing so is to eliminate troublesome foods, ride out a period of calm until symptoms settle, and then systematically reintroduce a single food to see if you can tolerate it.** Short of that, pick one, get started, and observe symptoms.

Stay in conversation with your functional medicine practitioner, certified coach, and/or nutritionist.

Note that no dietary protocol that supports autoimmune wellness should ever include gluten. Period. See “Non-gluten diet’ for an introduction if you’re unfamiliar with non-Celiac gluten sensitivity or the damage gluten does to the gut (which affects all autoimmune disorder, not just people with gut symptoms).

Paleo Diet

The core anti-inflammatory, nutrient-dense diet that helps prevent chronic illness.Emphasizes whole and organic, clean foods. Think “shop the perimeter of the grocery store.” 

Food groups excluded: Grains, Sugar, Dairy, Legumes, Processed food, Starches, Alcohol

Food groups included: Meat, Seafood, Vegetables, Fruit, Nuts & Seeds, Healthy Fats

Phased or steady? Steady

There are a lot of celebrity voices in this space, no shortage of recipes, online consumer suppliers3 and and even restaurants increasingly available.

Autoimmune Protocol (AIP)

Based on the Paleo diet, this protocol4 evolved through experimenters who researched and tested an elimination diet to calm autoimmune symptoms, upon which individuals can then build. There is now clinical proof5 of the efficacy of this approach in addition to a great deal of personal testimony. Quickly becoming the most on-point diet-based approach for autoimmunity.

Food groups excluded: In the elimination phase: Foods excluded in the Paleo diet plus: Eggs, Nightshades, Nuts, Seeds

Food groups included: Meat, Organ meat, Seafood, Vegetables, Fruit, Healthy Fats, Foods you find you can tolerate in the reintroduction process

Phased or steady? 2-Phased**

Founders include key players in the Paleo, Functional Medicine, and Autoimmune community.Great intros include The Paleo MomAutoimmune, and see ourResources Directory for many more.

Wahls Protocol

Standing also on the shoulders of those who’d gone before, The Wahls Protocol goes a step further in the specificity and volume of vegetables.7

Food groups excluded: Gluten, Casein, Albumin (egg white)

Food groups included: Heavier emphasis on vegetables, specifically, 9 cups per day from each of 3 groups (green leafy, brightly-colored, and sulfur-rich), Fermented foods and bone broth daily, Meat or fish

Phased or steady? Steady

Dr. Terry Wahls was wheelchair bound by MS when she began research into the Paleo diet and developed what became The Wahls Protocol. She is once again an active person today. Her TED talk is compelling.

Modified Paleo

Modified Paleo means, for most people, a predominantly Paleo diet, with a few additions that have been found not to trigger symptoms.

Food groups excluded: Paleo except: Safer-side additions

Food groups included: Safer-side additions can include: Non-traditional dairy (ghee, goat- or sheep-milk- based products, select fermented cows-milk products), Foods you find you can add after your elimination diet (wine? white potato?)

Phased or steady? 2-Phased** or Steady

Heroes in this category IMHO are groundbreaker Dr. David Perlmutter, author of Grain Brain, related texts, and leader in the functional medicine field for brain health.


A “Keto” / “low carb” / “low-carb, high-fat” diet is low in carbohydrates, high in fats, adequate in proteins. It was originally developed in the 1920s to control epilepsy but it since has been found to have greater applications, such as high blood sugar / insulin resistance, hormone imbalance, and cognitive decline. Popularly used for weight loss. Requires “adaption” by the body to a different process for generating energy and an awareness of when you’re in ketosis.9

Food groups excluded: Carbohydrates (including fruit), Processed foods, Grains, Conventional dairy, High-calorie beverages

Food groups included: Good Fats, Adequate proteins, Non-starchy vegetables, Full-fat dairy (ideally raw), See Dr. Axe’s Keto Foods List

Phased or steady? Steady

The body is prompted into ketosis by starving it of carbohydrates, in order to produce ketones in the liver to be used as energy, instead of the glucose / insulin cycle. So the body burns fat, vs. sugar. Translates predominantly to weight loss, but can aid health, including mental clarity, since the brain uses fat for energy.


A 30-day elimination diet that gets a lot of attention, good and bad, predominantly as a weight-loss plan.10

Food groups excluded: Paleo except: All sweeteners, incl. maple sugar and honey (allowed in Paleo), Baked goods or treats with approved ingredients (“subs = temptation”)

Food groups included: Paleo except: Processed foods that do not contain carrageenan, MSG, or sulfites, Fruit juice (discouraged in Paleo vs. whole fruit), Select legumes

Phased or steady? Set limit (30 days)

Co-created by Melissa Hartwig and Dallas Hartwig.


Predominantly for people with IBS, this diet is free of all high-FODMAP foods and emphasizes high-fiber, high-prebiotic foods. Specifically, “FODMAPs are a collection of short-chain carbohydrates (sugars) that aren’t absorbed properly in the gut, which can trigger symptoms in people with IBS.”11 Because it’s specific, it can take some time to get to know what’s in and what’s out (there’s an app for that).

Food groups excluded Examples: Apples, Avocados, Artichokes, Bananas, Beets, Cauliflower, Coconut, Garlic, Grapefruit, Mango, Mushrooms, Sweeteners, Onions, Peaches, Savoy cabbage, Shallots, Sweet potatoes, Watermelons

Food groups included: An equally specific list of alternative foods. Here’s a list. Note that a straight FODMAP diet includes foods that are typically excluded in an anti-inflammatory diet for autoimmunity, including soy and grain (and nuts, eggs, and dairy if in an elimination phase).11

Phased or steady? Set limit (30 days)

FODMAP stands for “Fermentable (gut process) Oligosaccharides (fructans+), Disaccharides (lactose), Monosaccharides (fructose), and Polyols (select sweeteners).” Whew. Monash University in Australia is a good governing resource for education and for   what’s compliant.12


Restricts selected starches, fruits, and vegetables, originally developed to address people with Celiac Disease, now more widely applied for gut disorders such as IBD, diverticulitis, and more. Takes some getting to know the specific exclusions and inclusions.

Food groups excluded: No grains, Specific list of disallowed: Meats, Vegetables, Fruits, Dairy, Starches/tubers, Spices – including curry, Sweeteners except honey

Food groups included: Specific list of allowed: Meats, Vegetables, Fruits, Dairy, Nuts, Legumes, Spices, Honey, Learn more about specifics or check the official list

Phased or steady? Steady

Based on the findings of Celiac researcher Dr. Sidney Valentine Haas in the first half of the 20th century, developed by author of Breaking the Vicious Cycle Elaine Gottschall, and made accessible today by SCD Lifestyle enthusiasts Jordan Reasoner and Steve Wright.


A relatively recent, next-generation interpretation of the SCD diet. Grains, starchy vegetables and refined carbohydrates are out; nutrient-dense foods that are easy to digest are in.13

Food groups excluded: Grains, Starchy vegetables, Refined carbohydrates

Food groups included: Phase 1: the most restrictive. Gradually add back foods through phases 2 through 6

Phased or steady? 6-Phased

GAPS stands for Gut and Pscyhology Syndrome, and it is rooted in treating the causes of Autism, though even since Natasha Campbell’s publication in 2004, the diet has found wider application such as for blood sugar regulation and reducing inflammation.


Gluten-free eating is the basic, Step #1 of using diet to help calm inflammation and autoimmune symptoms. Learn about non-Celiac gluten sensitivity from Dr. Tom O’Bryan.

Food groups excluded: Anything that has gluten in it: learn how to read labels here or, cut yourself some slack, and skip packaged goods as a rule. Learn about sources of gluten here.

Food groups included: Foods that do not contain gluten; get the definitely list from here (whether or not you’re Celiac)

See the same notes as for Modified Paleo. Although the impact of gluten had been known for some time, Dr. Perlmutter popularly awakened the world to the damage of gluten to the brain; Dr. Tom O’Bryan is also an international expert; both are active today.

Vegetarian AIP

Vegetarian diets can be hard to combine with an anti-inflammatory approach because of the need for protein while avoiding legumes (soy, peanut, lentils), eggs, nuts (at least at first), and a heavy reliance on grains. The good news is that nuts may be added back if symptom-free; see notes FMI.

Food groups excluded: Animal products, If vegan: dairy

Food groups included: Vegetables, Fruits, Nuts (if tolerated), Grains****

Phased or steady? Steady, or 2-Phased** if in combination with the AIP

Viktoria has a great blog on Vegan Health & AIP diet, and Eileen Laird of Phoenix Helix has a good discussion about the realities of marrying a vegetarian preference with autoimmune disease.  

Hybrid (a.k.a. The Best Diet for You)

The gold standard for arriving at The Best Diet for You is to:

  1. do an elimination diet***, and then
  2. add back one food at a time to see what you can tolerate.

Food groups excluded: You’ll start with a core set of foods that are typically not allergenic***, and then stay on them for 30 to 90 days until symptoms subside.

Food groups included: Once symptoms calm, typically at 30 to 90 days, you’ll follow a protocol for adding back one food at a time – typically starting with one you’ve missed – and watch for symptoms.***

Phased or steady? Steady, or 2-Phased**

In time, you may find that you can add back foods that you could not tolerate before — sometimes in small amounts, sometimes as part of your regular diet. Yay.


*The diets featured here are featured in the context of their support for autoimmune health. Weight loss is an outcome, but not a goal, of an anti-inflammatory diet or, more accurately, right-sizing is: you may gain weight as your gut heals and you become better able to absorb more nutrients if you’ve been chronically underweight from an autoimmune disease like IBD. If you’re overweight from hormonal imbalance, improper nutrition, inflammation, water retention, or all of the above, you’re likely to lose weight. But where weight management is a natural outcome of healthy eating, we don’t discuss “weight loss diets” since our context is combatting chronic illness.

**On a two-phase diet, there is typically an elimination phase followed by a reintroduction phase. The elimination phase is typically 30 to 90 days, during which time symptoms are expected to resolve. Then, you can enter a process of reintroduction, which typically allows for a single food at a time. If no symptoms appear after 72 hours of that food being reintroduced, you can add in a second new food. If symptoms do reappear, you reset to baseline before adding in another new food.

***There are two recommended options for an elimination diet:

1)    The Autoimmune Protocol (AIP), above, in which the first phase is an elimination diet and the second phase is reintroduction. The advantage of this diet is that it was specifically developed for people with autoimmune conditions, has a fair bit of road testing, and a lot of support around it for going through it as a process and getting specific recipes to counterbalance the sense of deprivation you can get when “giving up” your favorite foods (including a heavy emphasis on “picking up” new favorite foods).

2)    The Institute for Functional Medicine’s Elimination Diet. This is also a two-step approach with specific guidance about what’s in and what’s out, as well as how to reintroduce foods. See the handy one-page chart here.

I would caution you against trying ‘Susie’s Homemade Elimination Dietary Protocol’ — or whatever you might find wherever on the internet — because then you risk doing all that hard work and not getting the outcome and insight that are on-point. That’s not a good use of your time and resources.

Citations for more information:

1.    Ancestral diets as a broad category refer to dietary protocols that are rooted in the way our ancestors ate in the age before genetic modification, manufactured foods, pesticides, and herbicides entered the scene – which you might notice equates to the same timeframe in which the dominant world health issues transitioned from being about infection and acute care to chronic illness. Huh. Coincidence? Hence the proliferation of interest in a return to eating the way our ancestors did (plus all the ensuing evidence that it reduces inflammation and improves nutrition to do so). As always, there are iterations of diets, since people spend a great deal of time thinking about the best way to eat. At the end of the day, the best way to eat is the way that’s best for you to manage, reduce, or eliminate symptoms.

2.    Learn more in “What is the Paleo Diet?” by Robb Wolf, or by Dr. Sarah Ballantyne, a.k.a The Paleo Mom.

3.    Consumer sources for Paleo-compliant foods include Thrive MarketPaleo on the Go, OneStopPaleoShop, Barefoot Provisions, and Shop AIP. The definitive voice on the Paleo diet as it relates to Autoimmunity is Dr. Sarah Ballantyne of The Paleo Mom.

4.    Two good introductions to The Paleo Autoimmune Protocol (AIP) include those by Dr. Sarah Ballantyne (The Paleo Mom), and Mickey Trescott and Angie Alt ( Foods can be sourced through the same resources as in #3.

5.    The first clinical trial of the efficacy of The Autoimmune Protocol dietary impact on people suffering from autoimmune disease was conducted on people with IBD, who achieved favorable results. Published in the IBD Journal of the Crohn’s and Colitis Foundation in November 2017 by Gauree G. Konijeti, MD, MPH NaMee Kim, MD James D. Lewis, MD, MSCE et al.

6.    Founding contributors include Paleo diet pioneers Robb Wolf and Chris Kresser, researcher Loren Cordain, functional medicine practitioner Datis Kharrazian, researcher Sarah Ballantyne, and experiential learners and community leaders Mickey Trescott, Angie Alt, Eileen Laird, Whitney Ross Gray, and Christina Feindel. Learn more

7.    Dr. Terry Wahls discussed The Wahls Protocol as a recent guest on Straight Up PaleoWellness Mama’s post also gives a summary. There is a Wahls Warrior Parent Facebook Community (Wow! Kids eating 9 cups of vegetables and fruits a day!?).

8.    Modified Paleo “safer-side” food reintroductions might include a small amount, on occasion, of a favorite food that you find you can tolerate after doing an elimination diet. For example, see a discussion by Samantha Jo Teague of The Unskilled Cavewoman on Success with Dairy in Your Diet. Dr. Perlmutter’s Grain Brain Cookbook is another example of options.

9.     Dr. Axe’s site has a good summary of the Keto diet, or here’s a beginner’s summary of the Keto Diet and comprehensive resources by Craig Clarke et al on Note that “Our bodies are incredibly adaptive to what you put into it – when you overload it with fats and take away carbohydrates, it will begin to burn ketones as the primary energy source. Optimal ketone levels offer many health, weight loss, physical and mental performance benefits.” May be challenging for someone in a fragile autoimmune state. Dr. Mark Hyman, renowned leader of the functional medicine approach to chronic disease, began his early journey into functional medicine in part due to dramatic results he achieved with the Keto diet with a patient who’d seemed beyond recovery with neurodegeneration. A video by Dr. Hyman on the Ketogenic diet can be found here.

10. Here are the Whole30 Rules. Recent press like in US News* and Good Housekeeping have published articles against the Whole30 diet (using conventional food arguments as well as the fact that results are scientifically undocumented). Woman’s Day came out ”for”and Cosmopolitan came out “against.” Bottom line, it seems similar to a Paleo approach, but is focused on a different outcome – weight loss, vs. autoimmune support. Prevention discusses how to succeed on a Whole30 diet if you want to persist.

11. It can be daunting to apply a FODMAP diet as an added filter on top of an anti-inflammatory diet for autoimmunity (grain-, soy-, and dairy-free, plus possibly nuts- and egg-free to start). Luckily, there are bloggers who do that, by showing you which recipes are both Paleo or AIP and FODMAP compliant, for example. Using the particularly well-resourced meal-planning service Real Plans may be essential in this situation, where you can choose a dietary basis to follow, and then apply further food restrictions to take advantage of their robust search engine to do the menu planning for you. (Thank goodness for clever programmers being invested in healthy meal planning.)

12. FODMAPs and Irritable Bowel Syndrome by Monash University,

13. Learn more about the GAPS diet by Rachel Link, MS, RD on Dr. Axe’s blog or get the definitive orientation by the founder Dr. Natasha Campbell-McBride at

14. I prefer the term “non-gluten” to “gluten-free” as a dietary choice because it serves as a reminder that the goal is to seek foods that are naturally free in gluten, versus foods that are manufactured with grain substitutes and pseudo-grains that are loaded with sugar, undesirable oils, and gums to try to arrive at a facsimile of the gluten-containing original. Note that this doesn’t mean living without baked goods: there are a gazillion baked goods in the ancestral food diets that meet our need for the comfort foods and treats we grew up with – they just don’t contain grains, sugar, or gums. Nosh on.

Join our newsletter for our eBook – Honor yourself Autoimmune
No Thanks