It is said that we become like the top five people that we are closest too. It is hard to tell if we actually become like our best friends or if our pre-existing common interests help forge long-lasting friendships.

My top five friends and I are all health foodies. (No, we are not those selfie taking instagrammers who post every morsel they eat on Instagram). At dinner recently (in a very fairtrade, green organic restaurant) we all choose pretty much the same items from the menu. The irony was that (on that particular day at least ), we were all following different diets.

The elimination diet, the paleo diet, the autoimmune protocol, the 131 diet and the anti-inflammatory diet. That led to an animated debate (over greens and salmon) about the relative pros and cons of the different dietary approaches. If we were to be honest, we have all tried and been passionate about all of these diets at one stage or another over the last few years.

Of these diets, both the elimination diet and the autoimmune protocol are used in medicine. I decided to spend a little time researching the science behind these diets to see what all the fuss was about.

What Is A Paleo, AIP or Elimination Diet?

Common to the paleo, AIP and elimination diet is the concept of the ‘paleo deficit disorder’ (1). The general theory is that our manufacturing processes have outstripped our evolutionary capacity and our bodies are ill-equipped to handle processed, artificial foods that have clocked up bajillion of food miles.

Paleolithic Diet/ Stone Age Diet
The paleolithic and the primal blueprint diets are attempts to eat a nutrient dense diet which would be similar to the diet of our ancestors. The determining factor for inclusion of foods in the Paelo diet is whether a loincloth girded caveman with a twig would eat certain foods. Would Fred Flintstone have eaten this?  If the answer is yes, then it gets the green light. If the answer is no, then these foods would be avoided.

The paleo diet involves high quality, nutrient dense and whole foods, while avoiding highly processed, empty calorie, pro-inflammatory foods. The paleo diet is promoted by LeBron James and the Miami Dolphins NFL team (2).

These diets are naturally rich in wild game, wild greens, fruits and nuts which would have been the mainstay of food in the hunter-gatherer era.

There are some very funny articles in the medical literature about the paleo diet (which is unusual as the medical literature is usually very dry). Some people comment that our assumptions about the caveman diet are anthropologically and historically inaccurate. One particular article scathingly talks about ‘caveman soup’ and the PALEOf(x) conference where people can wear paleo clothes, cook with paleo cooking instruments and eat from ‘Cultured Caveman’ food trucks (2).

Elimination Diet
At the heart of the elimination diet is the belief that foods can trigger inflammation and disease. In many ways, it is closely related to the paleolithic diet theory. In this diet, people systematically eliminate certain foods from their diet to see if this improves their symptoms. The foods are then re-tested to see if the symptoms return. As such, the elimination diet is a clinical trial involving just one patient.

It is estimated that 35% of people in the developed world have some form of food hypersensitivity. The elimination protocol can be tried in people with multiple symptoms, medically unexplained symptoms, and also in people with a specific diagnosis.

The leaky gut syndrome is a popular (or should I say ‘trending’ explanation) for how food sensitivities affect us. According to the leaky gut brigade, our guts process antigens (foods). Tight junctions between the cells prevent macro molecules (foods) from crossing over into the systemic circulation (blood).

The tight junction between cells can become ‘leaky’ and allow antigens (food particles) crossover into the systemic circulation or blood. The tight junctions can become leaky due to food allergy, exposure to medications or change in the human microbiome. Once these macromolecules from food enter the blood, they can then elicit a systemic inflammatory response.

The theory with the elimination diet is that a subset of the population may be able to alleviate symptoms, slow the progression of their disease, reduce the use of medications, and have a heightened sense of control by eliminating certain foods from their diet.

There is nothing really new about this approach. Indian Ayurvedic medicine has prescribed the elimination of certain foods and the deliberate use of other foods for centuries.

The AutoImmune Protocol or AIP
The autoimmune protocol diet is essentially an extension of the paleolithic diet or a combination of the paleo-lithic and elimination diets. While it is based on the diet of paleolithic men, it is different to the standard paleo diet in that it is stricter in terms of the anti-inflammatory foods.

For example, it doesn’t allow tomatoes, peppers, eggs, nuts, seeds, and alcohol. (We will discuss allowed foods in more detail shortly). And secondly, it includes lifestyle factors such as management of stress, sleep hygiene, and social activity.

The overall goal of the diet is still to feed the body with nutritious food while avoiding pro-inflammatory foods. Foods that are encouraged on the autoimmune protocol are nutrient dense, promote a healthy microbiome, regulate the endocrine system and regulate the immune response in order to achieve a healthier microbiome, a healthy gut lining, and regulation of nutrients and hormones (that’s the theory).

Foods that are allowed on the autoimmune protocol include organ meat and offal, fish and shellfish, vegetables, herbs and spices, quality organic meats, quality fats, fermented foods, and a moderate fruit intake. Foods that are not allowed include grains, legumes, dairy, processed sugars, nuts, eggs, especially egg whites, and seeds.

Nightshades for example, tomato, eggplant, peppers, goji berries, potatoes (except sweet potatoes) are not allowed under the diet plan. A moderate intake of the following is allowed: omega-6 rich six rich foods, black and green tea, coconut and sugars such as maple syrup and honey.

Not only is the autoimmune protocol  a more strict or specific version of the paleo diet, it also extends beyond the actual diet to other aspects of a healthy lifestyle such as sleep hygiene, social support, and physical activity.

This underscores the growing recognition that there is not just a bidirectional influence of the brain on the gastrointestinal tract, and the gastrointestinal tract on the brain but that everything is interconnected.

The autoimmune protocol has four phases.
Firstly, the planning phase. This involves deciding which antigens or foods to eliminate, when to eliminate them and in which time sequence. Planning is essential as it takes quite a bit of commitment to do an elimination diet or an autoimmune protocol. This may involve purging food cupboards of the suspect food/foods to reduce the risk of food indiscretions.

In a regular weight loss diet, it is relatively easy to bounce back from a late night taco binge. Less so with the elimination or autoimmune protocol. Even a single exposure to the food (antigen) can trigger the inflammatory response and mess up the interpretation of the experiment.

Additionally, the planning phase involves scheduling the other health promoting activities that are part of the autoimmune protocol such as physical activity.

Secondly, the elimination phase, which as the name suggests, involves the elimination of common foods that can trigger intestinal inflammation, dysbiosis, or food intolerance. Common foods that are eliminated include the usual suspects of grains, legumes, dairy, caffeine, nuts, seeds, processed sugars, and food additives. Additionally, medications that can trigger any gut issues, for example, non-steroid anti-inflammatories are also ideally avoided. Fresh, nutritious foods and fermented foods are encouraged instead.

Thirdly, the reintroduction phase.This involves the gradual reintroduction of foods as tolerated. It is generally recommended that people wait until they feel significantly better, or at least wait for four weeks before attempting to reintroduce any of the eliminated foods. Symptoms that suggest a reaction, or food sensitivity could include any of the following: headache, fatigue, sugar cravings, low energy, bloating, anxiety.

It is recommended that only small amounts of the suspect food should be consumed during the re-challenge, or re-introduction phase. The aim is to slowly and safely increase the trial food gradually up to a full portion. Ultimately the plan is to reach a level of eating two to three portions in a single, 24 hour period. Then comes the waiting and watching phase – when people wait five to seven days to see if symptoms of hypersensitivity or reaction occur. During this time, it is essential not to reintroduce any other foods, as this will complicate the analysis.

The fourth stages of the elimination diet is longterm planning. The key to success in any diet is to shift from the perception of a diet ( which sounds temporary and like a sacrifice) to making the new eating pattern a lifestyle choice or way of living.

Is There Any Research?

There is only one published study looking at the auto immune protocol. To put this into context, there are 5034 publications on gluten free diets which include 209 human clinical trials. Before we give up too easily, the autoimmune protocol is really a stricter version of the elimination diet and the paleo diet.

There are 3673 publications related to the elimination diet, including 346 clinical trials. There are 212 studies on the paleolithic diet including 16 clinical trials.

We will consider all of these studies in our own research into the ‘paleo-deficit disorder’.

Does An AIP Diet Help Weight Loss?

There is nothing specifically on the autoimmune protocol helping with weight loss. A helpful GP review article summarized the data on weight loss with the Paeleo diet and looked at 4 trials including 126 patients. The overall conclusion was that the trials were underpowered but suggestive of some benefit in terms of weight loss (3).

Bottom Line

There are no well designed high quality studies looking at the effects of the AIP on weight loss. Underpowered studies suggest that the Paeleo diet may help with weight loss.

Does It Help Improve Gut Bacteria?

There is no great meta-analysis or clinical review that we can draw on here. We do have some interesting articles that can help us though.

A 2014 study in the Hazda of Tanzania (a hunter-gatherer community in East Africa) showed higher levels of microbial diversity and biodiversity than Italian control subjects (4). A really fascinating part of the study is the fact that the Bifidobaterium bacterial species is absent in Hazda adults which is thought to be due to an absence of meat and/or dairy in the diet.

Equally,there are differences between the gut microbiota between men and women which is though to be due to sexual division of labor and food in the tribe. This suggests that the hunter gatherer diet does impact on the gut microbiota.

Bottom Line

There is evidence that a hunter-gatherer diet can affect the microbiota but it is unclear as to whether this is a good, bad or neutral thing.

Does It Help Reduce Inflammation?

In this section, we will look at three different inflammatory conditions:

  1. Eosinophilic esophagitis
  2. Inflammatory bowel disease and
  3. Atopic dermatitis

Eosinophilic esophagitis is an inflammatory disorder which is triggered by food. Spanish investigators found that a 6 month 4 food group (dairy, wheat, eggs and legumes) elimination diet achieved clinicopathological remission (patients felt better and their biopsies improved too) in 54% of adult patients (5).

In a more recent study, non- responders to proton pump inhibitor therapy for esophinilic oesophagitis were offered either a 6 food elimination diet with a proton pump inhibitor or a steroid aqueous gel (6). The study found that  52% of patients who chose the elimination diet had a complete remission.

A 2017 study assessed the efficacy of the autoimmune protocol for inflammatory bowel disease (7). This US based study looked at the efficacy of the autoimmune protocol for different types of inflammatory bowel disease. Inflammatory bowel disease can be sub-classified as ulcerative colitis and Crohn’s Disease.

Diet is recognised as a risk factor for inflammatory bowel disease. Logically, given the close physical proximity of the food we eat to the gastrointestinal tract, it makes sense that adjusting diet may help reduce the inflammation associated with these conditions. This is pretty similar to avoiding asking contact with allergens in people with dermatitis.

This was an interesting single center, open label, uncontrolled study design. The study used a ‘SAD’ (standard American diet) to AIP (autoimmune protocol) in 6 weeks which they called the “SAD to AIP in 6’.

The patients were then followed up for 5 weeks on the new diet. The patients had access to a closed group on Facebook for education and peer support. They were also given books on the science behind the autoimmune protocol and recipes that they could use. Clinical remission was achieved in 73% of the study participants.

There was no difference in the achievement of remission between the Crohns and ulcerative colitis sub-groups of patients. Significant adverse events were noted in two patients. Both patients had structural damage to their gastrointestinal tract. Inflammatory bowel disease can cause narrowing or strictures.

The first patient had narrowing of a postoperative ileocolonic anastomosis (or surgical connection between the ileum and colon). The patient had to be admitted to hospital with partial small bowel obstruction which was thought to be due to the change in bowel habit associated with increased raw vegetable consumption. The second patient had a stricture of their ilececal valve and withdrew from the studies because of gastrointestinal symptoms.

The study had a number of limitations. The study was non-randomized and there was no control arm of the study. The authors concluded that dietary elimination can be helpful as adjunctive therapy in inflammatory bowel disease but that care needs to be taken with patients with anatomical abnormalities (see safety section below for more detail).

Adult patients with uncomplicated inflammatory bowel disease were randomized in a double blind study design (8). Patients were allocated to an elimination diet or a sham diet. Patients were tested for IgG antibodies to 29 different uncommon food antigens. The sham diet eliminated certain foods – but not the foods identified in the blood tests as potential allergens. The study took place over a period of 12 weeks. Patients in the true diet had a 10% statistically significant greater reduction symptoms severity.

A total of 93 of the study participants (41 in the true diet arm, and 52 in the sham diet arm) agreed to a phased reintroduction of foods that had been eliminated in the first phase of the study. Statistically significant more patients in the true diet as compared to the sham diet had worsening of their health during the reintroduction of the emitted foods.

Japanese investigators studied children with atopic dermatitis and found a decreased response of peripheral blood mononuclear cells and decreased IgE antibodies to egg of milk following an elimination diet (9).

Bottom Line

Available science suggests that an elimination diet may help with inflammatory diseases such as esinophilic esophagitis and inflammatory bowel disease.

Does It Increase Quality of Life for People With Autoimmune Diseases?

A 1997 paper stated that 30-40% of patients with rheumatoid arthritis respond well to elimination diets and that the response can occur within in 10 to 20 days (10). The article also stated that the symptoms of rheumatoid arthritis rebound once the trigger food is re-introduced. The paper compared the elimination diet to fasting and suggested that fasting is effective in the majority of patients and that the response can occur in as little as 3 days.

The author concluded that the mechanism of action of the elimination diet and fasting must be different given the different effects that these diets have on the target condition.

A Norwegian systematic review looked at the safety and efficacy of a range of dietary intervention for rheumatoid arthritis (11).

A total of eight randomized controlled trials with a total of 366 patients were included in the review. The authors concluded that the effects of the elimination diet in rheumatoid arthritis are uncertain due to inadequate data.

Bottom Line

A detailed review of the literature concluded that ‘effects of the elimination diet in rheumatoid arthritis are uncertain due to inadequate data’.

Does It Help ADHD?

The INCA study is a Dutch research project looking at the elimination diet in children with ADHD (13).

A total of 100 children were enrolled in a study and randomly assigned to 5 weeks of a restricted elimination diet or a healthy diet. Children with an improvement of greater than 40% on an ADHD rating scale were then challenged with foods as directed by their blood tests.

There was a statistically significant improvement in the ADHD score between the intervention and control group. Relapse occurred in 63% of the children on re-challenge. The relapse was not predicted by the blood test.

Bottom Line

An elimination diet may help children with ADHD. Before you shoot me, let me explain myself. Believe me when I say that I know how impossible it can be to do an elimination diet with a child with ADHD. Surviving day to day can be exhausting enough and fighting over favourite foods can be the final straw. Predictably, the foods that need to be eliminated are the favourite foods. All I am saying is that science shows that elimination diets may help. Practically speaking, this would take a lot of planning.

Does it Help With Migraine?

A Turkish study investigated the role of an elimination diet in patients with migraine and irritable bowel disease (12).

This was a randomized double blind cross over study in 21 women who were tested for over 270 food allergens. Study subjects were randomly allocated to either an elimination diet or a provocation diet. The elimination diet was associated with significant reductions in the number of attacks, attack duration and severity of attack of both migraine and irritable bowel disease.

Bottom Line

One very small study suggested that the elimination diet may help with migraine. This single study is not really robust enough to make a general recommendation but is all we have to go on for now.

Does it help Fibromyalgia?

Fibromyalgia is not classified as an inflammatory nor an autoimmune disorder and deserves a special mention. A small pilot study of just 8 women compared a healthy diet with an elimination diet. Both diets showed a trend towards a lower mean fibromyaliga score (14).

The elimination diet was associated with significant decreases in pain and stiffness.

Bottom Line

The elimination diet may help with fibromyalgia.

Is An AIP Diet Safe?

As mentioned above, special care needs to be taken with patients with anatomical abnormalities. There is a risk of obstruction in patients with narrowing of the gastrointestinal tract with the increased fecal load from the high-fibre diet.

Another potential risks of this protocol includes reactivation of a latent eating disorder. Orthorexia is a very real syndrome and possible risk of the autoimmune protocol. This is where people become obsessed with what they eat (anorexia is where people are fixated on minimizing calorie intake, while orthorexia relates to the content of what people eat).

It is imperative that any foods to which somebody has a significant allergy or anaphylaxis should not be reintroduced during the rechallenge phase.

Cost and time can also be issues as fast foods and processed foods are sometimes unreasonably cheap. Cost can also be an issue if only one member of a household is doing the autoimmune diet and needs special/extra foods as part of the autoimmune protocol. Micro nutrient deficiencies can occur but realistically this can also happen with the standard American diet as we well know.

Social isolation is another possible issue. It’s back to our friends again. It could be difficult to be all ‘paleo’ or ‘autoimmune protocol’ if your friends are having a beer and pizza movie night.


There are major similarities between many of the paleolithic inspired diets. Professionally speaking, I prefer the AIP over the over the other diets as I have yet to meet someone who just needs a diet adjustment as opposed to an overall lifestyle fix. I like the inclusion of sleep, stress reduction and physical activity alongside the food part of the diet.

While part of me is sceptical about cults and caveman fast food trucks, part of me gets it too. It is easier to belong to tribe, have a fancy recognizable name for your eating habits, have books to read and Facebook groups to belong to.

Overall, I think we are beginning to understand the real meaning of the Hippocrates advice ‘Let food be thy medicine and medicine be thy food’.

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