HomeSensitivity ScienceElimination Diets and Food Sensitivity

Elimination Diets and Food Sensitivity

(A rough introduction to the intriguing, evolving, and sometimes controversial science of food sensitivity)

If you’re wary of elimination diets simply because of the word diet, you’re on the right track. Diet is a troubled term.

We live in a toxic culture of body shaming. We’re constantly confused by the swinging pendulum of nutritional news coverage. Every year a new tide of diet trends crashes the bestseller lists and conquers Instagram. Keto much?

For all of these reasons I’m glad that ‘diet’—as in ‘I’m going on a diet’—is on its way towards becoming a dirty word. But our confusion about diet is all the more deranged because never have we been more certain that ‘diet’—as in ‘diet is a foundation for good health’—matters.

On this minefield I hesitantly share my opinion that an elimination diet can be a powerful tool for health. What you eat defines your diet. But for some people, some times, what you don’t eat is important too.

To emphasize: This is my educated opinion. I’m not a health care professional, and I’m not qualified to give medical advice. As a science journalist my skill set is asking questions, and my goal is to help you ask questions too. Health professionals are imperfect, and the good ones will acknowledge that they have an imperfect understanding of human biology. You need to ask questions if you’re going to get the full value from your health care dollar, because there are still quite a lot of unanswered questions about diet and health.

Perhaps even more essential, you need to ask yourself questions. Do you have health problems that may be triggered by diet? If so, is an elimination diet for you? They are powerful tools for discerning food intolerance, but require substantial patient effort. If you’re not willing to properly organize the experiment, or think critically about the results, then what’s the point? What are you going to do if you learn nothing at all?

The Are-We-There-Yet World of Nutrigenomics

Much of the emerging research about diet and health is circling around the idea that individuals have subtly different nutritional needs based on their genes, their microbiome, and their lifestyle. Using omics technology scientists can now decode DNA and other biological molecules faster than ever. Various names are in use for this emerging specialty: precision medicine, nutrigenomics, personalized nutrition.

The emerging evidence is fascinating: Your genes record the difference between eating fruit and drinking fruit juice.1 Your gut microbes are a big player in your risk of atherosclerosis.2 Some people appear to metabolize caffeine faster than others.3

For now the real winners are the rare few born with genetic malfunctions of metabolism. Doctors can now identify these issues and prescribe life-saving specialized diets.

Prescriptions for you and me are still a work in progress. Companies are already trying to sell dietary recommendations—just Google ‘nutrigenome testing’ and look at the sponsored links—but many researchers say the science is premature.4 But soon, perhaps even in the next decade, your doctor will analyze the genes in your body and in your gut to create a personalized eating plan for optimal health.

Maybe we’ll get that with our jet packs?

Cynical humor aside, I do see incredible promise in the scientific tools here. I believe that in my lifetime nutrigenomics—or whatever discipline it evolves into—will change the way many of us eat. But it’s a heavy lift: These are enormously complex systems, massively intertwined, and constantly changing. And it’s not clear that people without money will be able to access either the knowledge or the recommended menu.

Meanwhile here we are, right now, imperfect humans with our own imperfect knowledge, trying to stay healthy in our imperfect bodies.

And some of us suffer when we eat the wrong thing. Indeed, if you’ve read this far you’re probably at least wondering if you’re one of these people. The good news is that you’re already walking around in the best tool for detecting that sensitivity: your own body.

The Elimination Diet Goes Mainstream

Over the last decade, as scientists have been perfecting their DNA decoder rings, elimination diets have crossed into the mainstream.

An elimination diet strips a variety of plausibly harmful foods from your diet for a period of time, usually around 3 weeks, and then re-introduces them one by one. By keeping track of symptoms as you re-introduce foods, you may be able to determine if any of your symptoms are due to a particular food.

Elimination diets have been around in the medical literature since the 1930s, but have been minimally researched. No Betty Ford moment, no Angelina Jolie influencer has caused this current growth. Instead, elimination diets seem to have broken out naturally, fed by a variety of factors:

-Over the last several decades, food allergies have been growing more common, and elimination diets have a diagnostic role when allergen testing is inconclusive.
-Diagnoses of ADHD and autism have also been growing, and parents struggling with this have also employed elimination diets.
-Rates of inflammatory bowel disease—Crohn’s and ulcerative colitis—are increasing. No one-size-fits-all diet can control these conditions, but many people do manage them through trial-and-error food avoidance.

While all of this was developing, gluten intolerance became big business. Many people diagnosed their gluten sensitivity through elimination diets. Some diets were simple and self-administered, and some were supervised by health care providers. And gluten awareness has eased the way for other diet plans in popular culture. Whole30, FODMAP, The Inflammation Spectrum, paleo, and the autoimmune protocol (AIP) all have scientific ideas at their core, use elimination diets as a tool, and have thriving media empires.

While a lot of elimination dieting is DIY, there has also been an evolutionary embrace by the medical profession, and particularly through the growth of integrative medicine5 and functional medicine6. This paradigm shift includes many things, but its more holistic approach recognizes that patients are more than just biological systems, that lifestyle plays a role in disease development, and that doctors can and should provide solutions beyond their prescription pad.

Some doctors and skeptics7 fear that integrative medicine is more marketing than science. And no doubt, we all have to be on the lookout for marketing woowoo in medicine, and not just on the integrative side. But some skeptics also seem naïve of the contemporary efforts to validate many promising integrative techniques. Seeing the big picture also includes recognizing that lifestyle interventions are both harder to study, and harder to finance when there’s no blue pill to bank on. It is a work in progress and the challenge for integrative medicine is weeding out the promise from the pretenders.

Functional medicine gets special mention here because it makes a big deal of elimination diets. Practitioners write books and produce podcasts and videos, and their media-savvy presentations often claim elimination diets as their diagnostic starting point, and say that many patients heal themselves by tuning their diet. Skeptics complain that this is anecdotal evidence, and it’s true that this kind of marketing is something to be wary of, particularly when it’s presented out of context.

But the weight of observation—by doctors and patients alike—that elimination diets can work with complicated and hard to diagnose chronic conditions can’t be responsibly ignored. Furthermore, evidence of their utility is emerging from initial studies of their use in inflammatory bowel disease,8 eosinophilic esophagitis,9 migraine,10 and ADHD.11 Perhaps most importantly, medical science doesn’t have any better alternatives. There is not yet a complete explanation for the myriad cryptic symptoms that can be associated with food intolerance, and without that critical understanding scientists simply can’t build the tools to diagnose it.

Family doctors Suhani Bora and Adam Rindfleisch wrote about the alternatives in a chapter on elimination diets in the 4th edition of Integrative Medicine, a leading textbook in the field: “Aside from certain tests for IgE-mediated food allergies, most tests for adverse food reactions remain controversial. Such tests are more likely to discover clinically insignificant positive results, leading to unnecessary food restrictions, and to miss clinically important reactions.”12

Dr. Miranda Lomer, a leading PhD dietitian in the United Kingdom concurs, writing in a 2015 review: “The most helpful diagnostic test for food intolerance is food exclusion to achieve symptom improvement followed by gradual food reintroduction.”13

Orthorexia—A Careful Pause

A cautionary moment. Let’s begin with this warning from the Institute for Functional Medicine: “The Elimination Diet is not suitable for all patients. In particular, use caution when considering constitutionally weak patients, patients with acute illness, those with a history of disordered eating or an active eating disorder, and pregnant women.”14

Items 1, 2, and 4 seem self evident. But it’s worth spending a few extra moments on disordered eating.

Orthorexia nervosa is an obsession with healthy eating. According to the National Eating Disorders Association (NEDA) the term was coined in 1998, but is not yet not formally codified in the The Diagnostic and Statistical Manual of Mental Disorders published by the American Psychiatric Association. The NEDA website continues: “Although being aware of and concerned with the nutritional quality of the food you eat isn’t a problem in and of itself, people with orthorexia become so fixated on so-called ‘healthy eating’ that they actually damage their own well-being.”

It’s not incredibly difficult to imagine how this might begin. Food systems are enormously complex, and you don’t have to scratch too deeply to spot problems—ethical problems, economic problems, ecological problems, OMG-what-am-I-actually eating problems. If you then suspect that something you are eating might be causing you health problems, it doesn’t take much to send you on a witch hunt through your own cupboard.

Nightshades bring their own dynamic to the table because they are so prevalent, and because lax labelling laws allow them to remain hidden. Once my son’s two autoimmune diseases were diagnosed and I discovered that nightshades were triggering his most painful symptoms, I quite easily got worked up about ingredient labels, and had to spend a lot of time thinking about what he would eat and when. I quickly developed two signs of orthorexia.

It’s a difficult situation, particularly when mixed with some obsessive and/or compulsive tendencies. Add some social pressure and it becomes a real area of concern. For a revealing conversation about orthorexia—all the more powerful because it developed in two nutritionists who fully acknowledge they should have known better—listen to episode #83 of the Food Psych podcast.

If these dynamics strike an uncomfortable chord, you should consider a conversation with a trusted adviser, be that a doctor or a therapist, before you embark on an elimination diet.

Should You Consider an Elimination Diet?

Who should consider an elimination diet?

Bora and Rindfleisch (still writing in the 4th edition of Integrative Medicine) say that elimination diets may be useful with patients who have “multiple symptoms but no clear diagnosis,” when diet is known to aggravate symptoms for an already diagnosed condition, and where patients suspect sensitivity and may already be limiting their diets.15

The Institute for Functional Medicine suggests this laundry list of complaints: digestive problems, headaches, chronic sinus drainage, low energy, depression, mood swings, eczema, skin irritations, joint aches, asthma, and/or weight gain.

These common but cryptic symptoms can be associated with hundreds of medical conditions ranging from trivial to life threatening, and that’s why it’s a good idea to keep your doctor in the loop to rule out more serious conditions.

These symptoms may also be caused by food allergy and sensitivity. As many as 20% of Americans believe they have a food allergy or sensitivity, and diagnoses are increasing at epidemic rates.16 Food allergy, food sensitivity, and food intolerance are not the same thing, although academic literature is not entirely consistent on the precise differences. In food allergy minute amounts of the offending food can trigger a dangerous and very specific immune system reaction called anaphylaxis. (This is also called hypersensitivity, which is makes sensitivity a more complicated word to use.) Food intolerance is built more upon the idea that your digestive tract can’t handle a particular protein or compound in a food, such as lactose. What we’re learning is that our immune systems have myriad intertwined defense mechanisms. And because we don’t know how nightshade sensitivity works, we can’t actually label it.

You should be aware that this all-but-the-kitchen-sink approach to symptoms, and the still evasive underlying mechanism, invites scorn from some critics. And that might include your doctor. “Many doctors are not convinced that food allergy is a common problem, and some doubt that it even exists,” acknowledges Dr. Alan R. Gaby in the “Food Allergy And Intolerance” chapter of Integrative Medicine. These skeptics argue that many of these symptoms “fluctuate in severity and have a significant psychological component” making it difficult to tell a food reaction from a conditioned response or a sudden flush of symptoms. Because there is, as yet, no recognized or unifying scientific explanation, immunologists still even argue about what is technically “allergic.” This only emphasizes what we don’t know, argues Gaby: “[T]he more we learn about physiology, the more apparent it becomes how blurred the lines are between the immune system and various other bodily systems (such as the endocrine, nervous, and cardiovascular systems).”17

If you have any of the above symptoms and they’ve been nagging at you for longer than you care to admit, don’t be afraid of an elimination diet. But this is also the part where I remind you again that I’m not a doctor, and that talking with your doctor about these issues is a good idea. In particular, a doctor can help you identify whether your issues are truly chronic, or if you have a more immediate medical concern that would benefit from conventional treatment.


I’m not going to suggest a particular elimination diet approach here for one very important reason: the entire premise of this website is nightshade sensitivity. And if you have symptoms where elimination diet is suggested, the odds are that nightshades aren’t actually your problem. Other foods are more likely to be the culprit. I do believe it’s worth testing for nightshades because elimination diets are hard and the more complete your test, the more you are likely to learn.

If you’re working with a physician, you should plan your elimination diet with their help. If you’re going the DIY route, you can check some of the resources at the end of this essay.

To begin with you should spend some time recording your standard diet and your symptoms and looking for basic patterns.

I believe it’s important to practice food recording. Simply deciphering the ingredient label from your guilty-pleasure junk food, or trying to figure out the ingredients for your favorite take-out meal, will give you a low stakes chance to familiarize yourself with the complexity of the food system. Discovering a hurdle like that when you’re in the middle of an elimination diet can potentially derail the process. Understanding the challenge in your own diet helps set you up to succeed. You don’t need ninja-level nutritional wisdom. You do need enough information to determine potential candidates and weak spots.

Symptom recording is also important because that information provides a baseline health assessment that will help inform your test. A lot of people feel “better” during the elimination phase of their diet, but what does ‘feeling better’ actually mean? Being able to identify and quantify your results will make it easier to determine potential sensitivities. A more diverse diet is generally a healthier diet, so you don’t want to eliminate things without cause.

If you suspect a particular food—either from this initial journaling, or from previous learned experience—it’s probably worth testing. At least one experienced advisor believes that if you think you could never live without a particular food, you should test. Both of these observations trade on your body’s nutritional wisdom.

Nightshade sensitivity can be an outlier even in the world of people who use elimination diets. Not only do some elimination diets not recognize nightshades as potential bad actors, some list tomatoes and potatoes as go-to, safe foods. Gaby does not mention nightshades. Bora and Rindfleisch do with respect to rheumatoid arthritis, but caution there is limited evidence. Many elimination diets are built around the list of the 8 or 10 most common food allergies. Nightshade sensitivity may not be an allergy, and is probably rare. We just don’t know. You can understand why a book publisher might exclude it. But you should make your own decision about whether you should exclude it.

You can look here for a complete exploration of the science underpinning my argument that nightshades are worth testing, but the brief summary is this: Nightshade sensitivity is not classically allergic, so if you’re looking for allergy you may be using the wrong lens. Nightshades may affect the immune system via multiple pathways: There is plausibly an effect on one or more of the systems that control the gut.

If you’re going to go through the trouble of an elimination diet, I would argue that it simply makes sense to test for nightshades while you’re at it. It will make the elimination diet harder. But it should also increase your confidence in the results.

Planning an Elimination Diet

Full disclosure: I did not embark on a full elimination diet with either my son or myself. But hear me out!

For my son, I was daunted by the prospect of such a radically limited diet. He was dangerously thin, losing weight, in a great deal of discomfort, and not really old enough to understand the complexity of this approach. Because he ate very little outside of our kitchen, I was able to eliminate foods one by one over the course of about 5 months until we identified nightshades as the primary culprit. For me, I simply ate his nightshade free diet for a summer, and then reintroduced nightshades. (Mind. Blown.)

You can certainly use either of those approaches. The principals are the same. In fact, our diagnosis is arguably clearer because we didn’t do all of those other body cleansing things. In a fully implemented elimination diet, removing alcohol, caffeine, and reducing simple carbohydrates has a variety of other salutatory health benefits. “Of course you feel better,” say the skeptics. “Your blood sugar is under better control, your stress hormones are reduced, your blood pressure is reduced.” Your body is a more sensitive instrument under this regimen. But my father, daughter, and I have all been able to tell the difference simply by restricting nightshades.

But an elimination diet, while harder, is a more comprehensive lens. And as stated above, if you have symptoms that suggest an elimination diet, nightshades are not even the most likely culprit.

Here are some tips culled from experience, research, and conversation with other people using elimination diets:

KNOW YOUR WEAKNESSES: Is sugar or caffeine going to be your Achilles heel? Maybe alcohol? Plan your elimination diet to avoid triggering situations. Are you a book club aficionado who never misses book club, and always enjoys a glass of wine with your literary love fest? Plan your elimination diet around a book you don’t plan to read.

EASE IN: Sugar and caffeine are often connected at the hip. If you anticipate problems removing them, go slowly, and one at a time, until you’re ready to commence with the full elimination phase.

PICK YOUR TIME: If at all possible don’t try to pull an elimination diet during the holidays, during a deadline or a job change, during a divorce, or other stressful period.

PLAN TO COOK: Whether or not cooking is easy or fun for you, it’s going to be easier to successfully complete an elimination diet—and make use of what you learn—if you cook. Nightshades are a real challenge in restaurants and pre-packaged foods.

TAKE CARE OF YOURSELF: Sometimes we do things to make other people happy. If you get social pressure to abandon your elimination diet before you’re done, remember that you have the right to take care of yourself. Assert it.


There are a number of elimination diet resources online. These two began with work by David Rakel, editor of the Integrative Medicine text. Both come from the University of Wisconsin. Rakel is now the Professor and Chair of the Department of Family & Community Medicine at the University of New Mexico School of Medicine in Albuquerque, New Mexico.

The Elimination Diet, University of Wisconsin Integrative Health.

University of Wisconsin Integrative Medicine Elimination Diet

Here are a few more, including some from the Institute for Functional Medicine
Elimination Diet Food Plan

Simple Elimination Diet

Comprehensive Elimination Diet

Elimination Diet: Comprehensive Guide

There are also numerous books. I’ve read this one, so I’m comfortable recommending it as a general guide.

  1. Fruit and Juice Epigenetic Signatures Are Associated with Independent Immunoregulatory Pathways []
  2. Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota []
  3. PharmGKB summary: caffeine pathway []
  4. Nutrigenomics and the Future of Nutrition []
  5. Academic Consortium for Integrative Medicine and Health—History []
  6. The Institute for Functional Medicine []
  7. Science Based Medicine []
  8. Treatment of Crohn’s Disease with an IgG4-Guided Exclusion Diet: A Randomized Controlled Trial” ; “An Examination of Diet for the Maintenance of Remission in Inflammatory Bowel Disease []
  9. Current Approach to the Management of Eosinophilic Esophagitis in Adults []
  10. IgG-Based Elimination Diet in Migraine Plus Irritable Bowel Syndrome []
  11. Elimination diets’ efficacy and mechanisms in attention deficit hyperactivity disorder and autism spectrum disorder []
  12. page 852, Integrative Medicine, []
  13. Review article: the aetiology, diagnosis, mechanisms and clinical evidence for food intolerance []
  14. The Institute for Functional Medicine []
  15. page 849, Integrative Medicine []
  16. “Food Allergy: An Enigmatic Epidemic” []
  17. page 310, Integrative Medicine []


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