As a naturopathic doctor, one of the questions I hear most from parents is some version of: "Could this be something my child's eating?"

Tummy troubles, skin flare-ups, behaviour changes after meals — it's a completely reasonable thing to wonder about, and figuring it out matters, because a true allergy, a delayed-reaction allergy, and a simple intolerance are three different things with three different game plans.

Here's how to tell them apart, and what actually helps you get a clear answer.

First, let's untangle the terminology

Health Canada and the Canadian Paediatric Society sort food-related reactions into three distinct categories, and knowing which one you're dealing with changes everything about how it's managed.

Food allergy (IgE-mediated). This is the immune system reacting to a food protein, usually within minutes to a couple of hours, and it can range from mild to life-threatening.

The most common triggers are milk, egg, peanut, tree nuts, soy, wheat, fish, and shellfish.

Non-IgE-mediated food allergy. Still an immune response, but a different pathway — this includes things like FPIES (food protein-induced enterocolitis syndrome) and FPIAP (food protein-induced allergic proctocolitis).

These show up later, usually as gastrointestinal symptoms rather than the classic hives-and-swelling reaction.

Food intolerance or sensitivity. This one doesn't involve the immune system at all — it's usually about not being able to fully digest or absorb something, like lactose or gluten (in non-celiac gluten sensitivity).

Symptoms tend to be gut-related, dose-dependent, and not dangerous.

What each one actually looks like

The symptoms overlap more than you'd think, which is exactly why a detailed history — not a single test — is the real starting point for figuring out what's going on.

Signs of an IgE-mediated allergy:

  • Hives, swelling, or facial/lip/tongue swelling

  • Wheezing, trouble breathing, or throat tightness

  • Anaphylaxis (this is a medical emergency)

  • Symptoms that show up quickly after eating

Signs of a non-IgE-mediated allergy:

  • FPIES: delayed, forceful vomiting (1–4 hours after eating), lethargy, sometimes dehydration

  • FPIAP: bright red blood in the stool of an otherwise healthy, growing infant, usually in the first 6 months

Signs of a food intolerance:

  • Bloating, gas, cramping, diarrhea

  • Symptoms that show up later and scale with how much was eaten

If your child has been dealing with persistent eczema or unexplained skin flare-ups, food can sometimes be part of that picture too — I've written more about that connection in Eczema & Food Allergy Testing in Kids.

The testing question — and where a lot of families get steered wrong

This is genuinely one of the most important things to understand, because not all testing is created equal.

What the evidence actually supports:

  • A thorough, allergy-focused history — this is the real cornerstone of diagnosis.

  • Specific serum IgE and/or skin prick testing, interpreted alongside that history.

  • An oral food challenge, done under medical supervision — still the gold standard for confirming a true food allergy.

  • Celiac screening, if gluten intolerance is suspected (done before removing gluten from the diet).

  • A lactose hydrogen breath test, when lactose intolerance is suspected.

What allergy societies specifically advise against: 

Food-specific IgG and IgG4 testing is not recommended by the Canadian Society of Allergy and Clinical Immunology, the American Academy of Allergy, Asthma & Immunology, or the European Academy of Allergy and Clinical Immunology.

These tests largely reflect that your child has eaten a food and tolerated it — not that it's causing a problem. Acting on them can lead to unnecessary food restriction, which in a growing child can mean real nutritional gaps.

Applied kinesiology and electrodermal testing fall into the same not-evidence-based category.

The gold-standard approach: elimination and reintroduction

When an intolerance or non-IgE-mediated reaction is suspected, a supervised elimination diet followed by a structured reintroduction (or a formal food challenge) is the approach the evidence actually supports.

For suspected non-IgE cow's milk allergy in infants specifically, there's a well-established protocol for exactly this process.

A few things worth knowing if you're heading down this road:

  • Cutting out multiple food groups at once carries a real risk of nutritional gaps — calcium, vitamin D, and iron are the ones to watch.

  • Having a professional involved (ideally including a registered dietitian) during an elimination diet matters, especially with young kids.

  • Follow-up matters just as much as the elimination itself — reintroducing foods as soon as tolerance is confirmed avoids restricting longer than necessary.

If milk is the food in question, it's also worth a look at Is Your Child Drinking Too Much Milk? — sometimes the issue isn't an allergy at all, just an intake balance question.

Once you have an answer

If a true allergy is confirmed, management typically includes a written action plan for caregivers, school, and childcare providers, and — where there's an anaphylaxis risk — an epinephrine auto-injector.

For non-IgE cow's milk allergy, an extensively hydrolyzed formula usually does the job well, with amino-acid formula needed only occasionally.

For select children aged 4 and up with a persistent, confirmed allergy to peanut, egg, or cow's milk, oral immunotherapy under specialist supervision is another evidence-backed option worth discussing.

When to seek care right away

Some symptoms mean it's time to act, not wait and watch:

  • Trouble breathing, throat tightness, or facial swelling — call emergency services

  • Blood in the stool

  • Forceful, repeated vomiting, lethargy, or signs of dehydration

  • Weight loss or a stall in growth

  • Severe eczema that isn't responding to standard treatment

The bottom line

Figuring out whether your child has a true allergy, a delayed allergic reaction, or a simple intolerance starts with a thorough history from a practitioner who knows what to ask — not a broad panel test.

From there, specific IgE or skin prick testing, and sometimes a supervised food challenge, fill in the rest.

IgG "sensitivity" panels, despite being widely marketed, aren't backed by the evidence and tend to create more restriction than answers.

If your child's eating patterns have you wondering about something beyond allergies, it's also worth reading Is Your Child a Picky Eater? — food refusal and true reactions can look surprisingly similar from the outside.

FAQ

What's the difference between a food allergy and a food intolerance? An allergy involves the immune system and can happen quickly, sometimes severely. An intolerance is about digestion — usually gut symptoms that build with the amount eaten, and not dangerous.

Are IgG food sensitivity tests worth doing? No — major allergy societies advise against them. They tend to reflect food exposure rather than a real problem, and acting on the results can lead to unnecessary dietary restriction.

What's the best first step if I suspect a food reaction? A detailed history with a practitioner familiar with children's food reactions, followed by targeted testing if it's warranted — not a broad panel test done on its own.

Can a food intolerance turn into something more serious? Intolerances themselves aren't dangerous, but any time symptoms are severe, sudden, or involve breathing or swelling, that's a different category and needs emergency care.

If you're concerned about food-related symptoms in your child, I'd be glad to help you sort through it.

Book a consultation — in-person in Barrie or virtually anywhere in Ontario — and together we'll take a proper history, arrange the right testing, and build a plan that keeps your child's nutrition on track.

This post is for educational purposes only and does not constitute individual medical advice. Always consult a qualified practitioner for a personalized assessment.