How FPIES Differs from Food Allergies, Celiac, and Intolerances in Babies

As a pediatric food allergy specialist, I often meet families who feel overwhelmed trying to understand their child's reactions to different foods.

Is it an allergy? 
A sensitivity?
Something else entirely?

If you’re wondering the same things, you're not alone, and the better news is that once you know the difference between conditions like IgE-mediated food allergies, food protein induced enterocolitis syndrome (FPIES), lactose intolerance, celiac disease, and food sensitivities, navigating your child’s needs becomes much clearer.

Let’s walk through each condition, highlight how they are similar, and - more importantly - how they are different.

IgE-Mediated Food Allergies: The Classic “Food Allergy”

Understanding the immune reaction behind classic food allergies

When most people think of a "food allergy," they are thinking of an IgE-mediated food allergy. This involves the immune system reacting to a food protein as if it were a threat. Food-specific immunoglobulin E (IgE) antibodies bind the food and allergy cells, triggering those allergy cells to release chemicals that cause symptoms of an allergic reaction.

To understand more about how early food introduction can influence these types of allergies, this article explores whether early introduction helps prevent food allergies in infants.

The telltale signs of an IgE allergy in babies and toddlers

Symptoms usually come on within minutes, but can arise up to 4 hours after ingestion. Symptoms may be:

• Hives

• Swelling

• Vomiting

• Itching

• Dizziness

• Low blood pressure

• Trouble breathing

Experiencing more than one symptom at a time is considered “anaphylaxis”, which can be life-threatening if not identified and treated quickly.

Common foods that trigger allergic reactions in infants

Common culprits include:

• Peanuts

• Tree nuts

• Milk

• Eggs

• Wheat

• Soy

• Fish

• Shellfish

• Sesame

How food allergies are diagnosed (and what support looks like)

Diagnosis typically involves skin prick testing, blood tests measuring food-specific IgE levels, and/or an oral food challenge supervised by a pediatric allergist.

Management means strict avoidance of the allergen and carrying an epinephrine auto-injector or nasal epinephrine spray for emergencies. There are other treatments available now, including:

• Oral immunotherapy (OIT)

• Omalizumab injections

• Other emerging therapies like SLIT and EPIT

If you’re beginning this journey, here are 6 expert tips for safely introducing top food allergens to your baby.

What is FPIES (Food Protein-Induced Enterocolitis Syndrome)? The less-known food allergy that starts in the gut

How is FPIES different from a typical food allergy?

FPIES is a different kind of food allergy. It does not seem to involve IgE antibodies, and it primarily affects the gastrointestinal tract.

What foods can trigger FPIES

Common triggers include:

• Cow’s milk

• Soy

• Rice

• Oats

• Banana

• Sweet potato

• Peanuts

• Egg

• Shellfish

FPIES symptoms in babies to watch out for (even hours later)

Symptoms are very different from typical food allergies and occur 1–4 hours after eating, often including:

• Repetitive, severe projectile vomiting

• Diarrhea

• Pale appearance (pallor)

• Lethargy (limp, poorly responsive or unresponsive child)

• Notably: No hives or swelling are present

Why timing matters when FPIES symptoms usually start

Symptoms usually begin 1–4 hours after eating, which is one of the key ways FPIES differs from IgE allergies.

How FPIES is diagnosed without a standard test (yes, that’s normal)

Diagnosis is made based on clinical history, because there are no specific tests available for this disease. Sometimes an oral food challenge under medical supervision is needed to confirm the diagnosis. This is only done by a pediatric allergist who has experience with FPIES.

For a deeper dive into FPIES, this detailed guide explains how it fits into your child’s food allergy journey.

What FPIES management looks like — and why most kids outgrow it

Management involves:

• Avoiding trigger foods

• Creating an emergency plan

Many children outgrow FPIES on their own by age 5.

Milk trouble? The difference between lactose intolerance and milk allergy

What lactose intolerance really means (it’s not an allergy)

Unlike allergies, lactose intolerance does not involve the immune system at all. Instead, it’s a digestive issue where the body doesn’t produce enough lactase, the enzyme needed to break down lactose (milk sugar). Although this disorder can cause discomfort, it is never life-threatening like an IgE-mediated milk allergy.

How to spot lactose intolerance symptoms in babies

Symptoms typically show up 30 minutes to 2 hours after consuming dairy and include:

• Bloating

• Gas

• Diarrhea

• Stomach cramps

Gentle strategies for managing lactose sensitivity in your little one

Diagnosis can be made with:

• A hydrogen breath test

• Lactose tolerance test

• Symptom improvement after removing lactose

Management involves reducing or eliminating lactose-containing foods. Many kids tolerate:

• Lactose-free milk

• Hard cheeses

• Small amounts of dairy

🔍 Important to note: Lactose intolerance is NOT an allergy to milk proteins, so it’s different from a milk allergy (which can cause life-threatening anaphylaxis).

Celiac disease in babies is an autoimmune disorder, not a food allergy

What happens in the body during celiac disease

Celiac disease is an autoimmune condition, not an allergy. When someone with celiac eats gluten (a protein found in wheat, barley, and rye), their immune system inappropriately attacks the lining of the small intestine, leading to long-term inflammation of the bowel and damage.

Possible signs of celiac in babies (hint: it’s not just tummy trouble)

Symptoms vary widely and may include:

• Chronic diarrhea or constipation

• Abdominal pain

• Poor growth

• Fatigue

• Iron-deficiency anemia

• Rashes

How doctors test for celiac

Diagnosis involves:

• Blood tests looking for specific antibodies (like tissue transglutaminase IgA)

• A biopsy of the small intestine, typically performed by a pediatric gastroenterologist

What life looks like on a gluten-free diet (one step at a time)

Management requires a strict, lifelong gluten-free diet. Even tiny amounts of gluten can cause harm, even if symptoms aren't obvious.

Not All Reactions Are Allergies: How to Spot Food Sensitivities in Babies

What we know (and don’t) about food sensitivities in infants

Food sensitivities (sometimes called food intolerances) are less clearly defined. They don’t involve the immune system in the same way allergies do, and reactions are often dose-dependent — the more your child eats, the worse they feel.

Common triggers and symptoms of baby food sensitivities

Examples include:

• Certain food additives (e.g., sulfites)

• Specific foods that are hard to digest

Reactions are often delayed and may include:

• Abdominal pain

• Headaches

• Fatigue

Why testing isn’t recommended — and what to try instead

There are no validated tests for food sensitivities. Tests marketed to identify food sensitivities using food-specific IgG are not reliable. In fact, IgG molecules can sometimes indicate food tolerance rather than intolerance.

Pediatric food allergists do not recommend these tests for children. Eliminating several foods after IgG testing can be dangerous for developing children.

Safe, simple ways to explore sensitivities without over-restricting

Instead, the gold standard is:

• Single food elimination diets

• Careful reintroduction guided by a pediatric specialist

Management often involves limiting - but not always completely avoiding - the problematic food.

Fpies vs allergy, intolerance, celiac & sensitivity: a side-by-side comparison

How to Feel Confident Navigating Your Baby’s Food Reactions

Understanding the differences between food allergies, intolerances, and sensitivities can be life-changing for your family.

• If your child has rapid, serious symptoms like hives, swelling, or difficulty breathing after eating, seek immediate medical attention.

• If the reactions are mostly digestive or delayed, it may point toward FPIES, lactose intolerance, or a sensitivity.

• If you suspect celiac disease, talk to your pediatrician before removing gluten from your child’s diet, as accurate diagnostic testing requires the child to have been eating gluten.

You don't have to figure it out alone. Your child’s pediatrician, pediatric allergist, or gastroenterologist can help you get a diagnosis and create a safe, nourishing plan for your child. Every child deserves to enjoy food safely and comfortably.

For a quick guide that recaps the key differences between allergies, intolerances, and sensitivities, this article is a helpful place to start.

Written by Dr. Taylor Lin

Pediatric Allergist & Advisor at Bébé Foodie

 

Meet Dr. Taylor Lin, our go-to expert on allergies and immunology! Dr. Lin serves families in southeast Michigan as an allergy and immunology physician with Allergy & Immunology Associates. With top-notch training from the University of Michigan and a specialty fellowship in pediatric food allergy, she’s not just highly qualified—she’s also a mom to a child with food allergies herself! Dr. Lin directs her clinic's food oral immunotherapy program and brings evidence-based, accessible advice to families through her role with Bébé Foodie.

 

This blog post is for information purposes only and shouldn’t be used as personal, health, nutritional, or medical advice. Always consult with your pediatrician before making any decisions about your child's health or readiness for various foods.