Elimination diets are everywhere—from parents managing eczema to influencers cutting out gluten and dairy in pursuit of “clean eating.”
But research shows that removing foods from your diet can subtly change how your immune system reacts when you eat them again. In some people, especially those with conditions like eczema or past food allergies, that loss of tolerance can spark dangerous reactions—even life-threatening anaphylaxis—when the food returns.
This risk is often overlooked in the growing popularity of elimination diets. According to the CDC’s National Center for Health Statistics, Americans are cutting more from their plates than ever. Some do it to manage celiac disease or irritable bowel syndrome, others to reduce bloating, fatigue, or joint pain. Social media trends like #cleaneating have only amplified the appeal. By 2024, more than half of Americans reported following a specific diet or eating pattern, compared to just 38 percent in 2019.
Yet for the immune system, regular exposure to food proteins helps maintain a state of tolerance—one that can be disrupted when those foods disappear from the menu for too long. Understanding how and why that shift happens is key to knowing when elimination diets help, and when they might put you at risk.
The science of oral tolerance and food allergies
“The intestine has an unenviable task,” says Brian Vickery, chief of allergy and immunology and director of the food allergy program at Emory’s Children’s Healthcare of Atlanta. “It has to identify and respond to a constant barrage of environmental stimuli that can be both dangerous and beneficial.”
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The gastrointestinal tract, which has more immune lymphocytes than any other body part, encounters trillions of microbes and more than 30 kilograms of food proteins each year. Yet, it manages to defend against harmful invaders while ignoring harmless foods and friendly bacteria.
This balancing act relies on oral tolerance, a process in which immune responses to ingested food proteins are actively suppressed, which in turn prevents harmful reactions like food allergies. While the underlying immune mechanisms are not entirely understood, the latest studies indicate it begins with specialized antigen-presenting cells that capture food antigens in the gut and instruct nearby T cells to stand down. This signal gives rise to antigen-specific regulatory T cells, which calm the immune response to food proteins.
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“The gut is important in the initial establishment of tolerance,” says Michael Pistiner, director of Food Allergy Advocacy, Education and Prevention, Food Allergy Center at the MassGeneral Hospital for Children. “If you’re not already allergic, early introduction to foods can help promote tolerance and protect infants from developing a food allergy.”
That protection doesn’t end in childhood. Regular, ongoing exposure to foods helps maintain oral tolerance throughout life. Recent research in food allergy patients treated with oral immunotherapy, where gradually increasing doses of the culprit food are given orally, highlights how continued ingestion is often needed to maintain a desensitized state. Conversely, there’s evidence that elimination diets for some can disrupt oral tolerance and encourage the immune system to develop allergies.
When elimination diets increase allergy risk
For parents of children with eczema, it’s common to suspect certain foods are worsening flare-ups. Many turn to elimination diets in hopes of finding the culprit. But research has uncovered a hidden risk. Anne Marie Singh, professor and chief of Division of Allergy, Immunology, and Rheumatology at the University of Wisconsin-Madison, and her colleagues evaluated almost 300 children with eczema on elimination diets.
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“We found that if you removed the food from their diet, upon reintroduction there was a significant increase in the risk of allergic reactions, including potentially severe immediate allergic reactions,” says Singh. The results were striking: almost one in five children (19 percent) developed new immediate allergic reactions when the eliminated foods were reintroduced, even though they had no previous history of such responses. Most were mild, but alarmingly, 30 percent of reactions were severe, classified as anaphylaxis.
The danger isn’t limited to children. In a separate study of 30 adults who developed allergies to foods they had previously tolerated, 70 percent had been on elimination diets beforehand. Half experienced anaphylaxis, and the vast majority (80 percent) had pre-existing allergic conditions such as environmental allergies, asthma, or eczema. For people without a history of allergies, the risk appears much lower.
What to know before starting an elimination diet
If you’re thinking about trying an elimination diet, experts say the safest approach depends on your risk level. If you’re at higher risk (children or anyone with pre-existing allergy conditions), consult with a healthcare professional before starting an elimination diet.
“The more allergic you are, an elimination diet could potentially be a problem,” says Singh. Pistiner adds that “in infants with eczema, elimination diets can be detrimental, especially at this very important time of early introduction.” Experts also recommend that children following elimination diets have close medical supervision to ensure nutritional adequacy and healthy growth.
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Duration matters, too. A shorter elimination phase gives less time for oral tolerance to break down. Singh notes that “two to four weeks of elimination should be enough time to know if it makes a difference and also short enough to not risk an allergic reaction when you try it again.”
In some cases, completely cutting out a food isn’t necessary. If symptoms are mild, keeping small, tolerable amounts in the diet may help maintain oral tolerance while still easing discomfort, adds Singh.
