The world of dietary protocols can be overwhelming, especially when two approaches, like Paleo and AIP, seem to overlap. While they both emphasize real food and nutrient density, their purposes are distinct. Understanding their differences is especially important if you’re dealing with chronic inflammation or autoimmune disease.
Let’s explore what sets these protocols apart, the science behind them, and how to choose the one that’s right for you.
Paleo Diet: Back to Ancestral Basics
The Paleo Diet is designed to mimic the eating habits of our pre-agricultural ancestors. The core belief is that many modern diseases, particularly inflammatory and metabolic disorders, stem from the introduction of processed foods, grains, refined sugars, and industrial seed oils that were never part of the human diet until very recently.
From an evolutionary biology perspective, humans have existed as hunter-gatherers for roughly 2.5 million years. Agriculture, and with it, the widespread consumption of grains, legumes, and dairy, only emerged around 10,000 years ago. Even more recently, ultra-processed foods, seed oils, preservatives, and artificial sweeteners have become dietary staples over the last 100 years, comprising the bulk of the modern diet despite being largely foreign to human physiology for the vast majority of our history.
The Paleo approach aims to return us to a more evolutionarily appropriate way of eating—one that our digestive, immune, and metabolic systems are biologically adapted to handle.
Paleo allows:
- Grass-fed meats and wild-caught fish
- Organic vegetables and fruits
- Eggs
- Nuts and seeds
-
Healthy fats (e.g. olive oil, coconut oil, avocado)
It avoids:
- Grains (including wheat, oats, corn, rice)
- Dairy products
- Legumes (beans, lentils, peanuts)
- Refined sugars and processed foods
-
Industrial seed oils (like canola, soy, safflower)
The Paleo diet emphasizes whole, nutrient-dense foods that support metabolic health, stable blood sugar levels, and reduced inflammation. While not designed as a clinical protocol, many people experience improvements in digestion, energy, and inflammatory symptoms simply by removing modern irritants and increasing nutrient density.
The Autoimmune Protocol (AIP): A Therapeutic Strategy for Autoimmunity
AIP is a more targeted, science-informed version of Paleo developed for individuals with autoimmune disease or symptoms of chronic inflammation. It incorporates the foundational principles of Paleo but takes them further to eliminate even more immune-reactive and gut-disrupting foods.
Why? Research has shown that autoimmune disease often involves increased intestinal permeability ("leaky gut"), nutrient malabsorption, and an overactive immune response. AIP is designed to remove foods that exacerbate those issues and add in those that support tissue repair, immune modulation, and gut barrier integrity.
The Core Elimination Phase of AIP avoids everything Paleo does, PLUS:
- Eggs (which can provoke immune reactions)
- All nuts and seeds (including coffee, chocolate, and seed-based spices)
- Nightshades (tomatoes, potatoes, peppers, eggplant)
- Alcohol and NSAIDs (which irritate the gut lining)
-
Food additives and emulsifiers
AIP focuses on:
- Repairing the gut lining
- Regulating immune system activity
- Identifying individual food triggers through reintroduction
-
Supporting detoxification and nutrient repletion
AIP is not meant to be followed indefinitely. It's structured into two phases:
- Elimination Phase – Remove inflammatory triggers and flood the body with nutrients.
- Reintroduction Phase – Gradually reintroduce foods to identify what your body tolerates.
This makes AIP more than just a diet; it’s a clinical nutritional intervention for immune regulation and symptom resolution.
Modified AIP: The 2024 Consensus
In 2024, leading practitioners introduced Modified AIP (mAIP) based on clinical observations. Over time, it became clear that certain foods, like white rice, ghee, and properly prepared legumes, were well tolerated by most clients. Modified AIP offers more flexibility while still aligning with the core therapeutic goals of AIP, making long-term adherence more accessible.
Importantly, this version of AIP diverges from Paleo even further, as Paleo does not include legumes or rice.
Side-by-Side Comparison
|
Paleo |
AIP (Elimination Phase) |
|
|
Purpose |
General health and inflammation |
Therapeutic intervention for autoimmunity |
|
Removes Grains |
✅ |
✅ |
|
Removes Dairy |
✅ |
✅ |
|
Removes Eggs |
❌ |
✅ |
|
Removes Legumes |
✅ |
✅ |
|
Removes Nightshades |
❌ |
✅ |
|
Removes Nuts/Seeds |
❌ |
✅ |
|
Reintroduction Phase |
❌ |
✅ |
|
Focuses on Gut Healing |
❌ |
✅ |
|
Allows Rice/Legumes (mAIP) |
❌ |
✅ (Modified AIP only) |
So, Which Protocol Is Right for You?
Choose Paleo if:
- You’re seeking a whole-food approach for general health, metabolic support, or weight loss.
-
You don’t currently have an autoimmune condition or significant digestive issues.
Choose AIP if:
- You’ve been diagnosed with an autoimmune disease or are dealing with symptoms like fatigue, joint pain, skin flares, brain fog, or chronic gut issues.
-
You want to identify your personal food triggers and reduce inflammation more strategically.
At their core, both dietary approaches share a foundation of whole, nutrient-dense eating, removing common inflammatory foods such as gluten, grains, and dairy, as well as all processed foods. Other dietary protocols follow similar foundations, whether it be the Whole30 or Mediterranean diet, to name a few. But while AIP is called a diet, it should be thought of as a bi-phasic, nutritional protocol, specifically tailored to support autoimmune healing. If you're living with an autoimmune disease, AIP offers a structured and research-informed approach to reduce inflammation, support your immune system, and identify the foods that work best for your body.
However, keep in mind that transitioning to AIP doesn’t have to be a cold turkey approach. Many people start with a Paleo elimination and then work their way into eliminating the rest of the foods to reach full core AIP compliance. You don’t have to jump in all at once!
The key here is to determine the best option for you to achieve success in reaching your goal.
Want to know if you are a Cold Turkey or a Slow transition type of person? Take the quiz here! https://www.aipsummit.com/opt-in
If you’re unsure where to start, it’s always helpful to consult with a functional nutrition practitioner or AIP Certified Coach to determine which protocol fits your needs and health goals.
And if you need help staying on track with AIP meals, Urban AIP is here to help. We take the guesswork out of mealtime with delicious, fully AIP-compliant meals delivered to your door.
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