What are food sensitivities, intolerances and allergies? Symptoms, causes and a functional medicine approach

Food allergies, sensitivities and intolerances are three distinct types of food reactions, each involving different physiological processes and producing different patterns of symptoms.

A food allergy occurs when the immune system identifies a food protein as a threat and mounts a defensive response. A food sensitivity involves a slower immune response, through a different antibody pathway, rather than the rapid reaction of a true allergy. It does not carry the same life-threatening risk but can still cause significant and wide-ranging symptoms. Whereas a food intolerance works differently from both and typically develops when the body lacks the enzyme or compound needed to digest a specific food. We’ll dive deeper into the differences between the three below.

What’s the difference between a food allergy, sensitivity and intolerance?

Food reactions fall into three categories, each involving a different process in the body.

Food allergy (immediate hypersensitivity)

A true food allergy is a fast immune reaction, also known as an IgE-mediated immune response. The immune system produces IgE antibodies against a specific food protein, which triggers immune cells called mast cells to release histamine. Symptoms appear within minutes to an hour and can include:

• Hives, itching or skin flushing
• Sneezing, coughing or watery eyes
• Shortness of breath and asthma-like symptoms
• Swelling of the lips, tongue or throat
• Anaphylaxis – a life-threatening reaction involving throat swelling, rapid blood pressure drop and loss of consciousness, requiring emergency adrenaline treatment

Susceptibility to food allergies often runs in families. The most common allergens include peanuts and tree nuts, dairy, egg, fish, shellfish and seafood, and soy.

Food sensitivity (delayed hypersensitivity)

Food sensitivities involve a different arm of the immune system. Instead of IgE, the body produces IgG antibodies, and the immune response that follows is slower and lower-grade, more of a simmering reaction than an immediate one. Symptoms are not life-threatening but can be wide-ranging and persistent. Key features:

• Reactions can appear anywhere from 90 minutes to 72 hours after eating
• The delay makes identifying the trigger food genuinely difficult
• Symptoms can affect digestion, skin, energy, mood and cognition
• Symptoms often are not specific to the digestive system
• Symptom flares in other inflammatory conditions (e.g. arthritis, psoriasis)
• Non-coeliac gluten sensitivity is a well-recognised example

Food intolerance

A food intolerance does not involve the immune system. It occurs when the body lacks the enzyme, compound, or cofactor needed to break down a particular food. Key features:

• Symptoms are mostly digestive
• Reactions are often dose-dependent – small amounts may be tolerated, larger amounts cause symptoms
• Lactose intolerance, where the enzyme lactase is insufficient to digest milk sugar, is the most common example

Symptoms of food allergies, sensitivities, and intolerances

Symptoms from food can affect multiple body systems, and the reaction can vary between individuals. Two people with the same reaction type can experience very different symptoms, in both presentation and severity.

Food allergy symptoms

Food allergy symptoms tend to appear within minutes to a couple of hours of exposure and can range from mild to life-threatening.

Skin:

• Hives – raised, itchy, red welts
• Deep swelling around the face, eyes, lips or throat (angioedema)
• Eczema (atopic dermatitis)
• Psoriasis

Respiratory:

• Sneezing, runny nose, sinusitis
• Watery or itchy eyes, conjunctivitis
• Difficulty breathing, asthma

Digestive:

• Nausea, vomiting
• Diarrhoea (Frequent)
• Flatulence, colic, abdominal pain
• Constipation (less common)

Systemic:

• Fatigue, headaches, migraines
• Mood and behavioural changes
• Low blood pressure, rapid or reduced heart rate
• Anaphylaxis – throat swelling, sudden blood pressure drop and loss of consciousness, requiring immediate adrenaline treatment

Food sensitivity symptoms

Food sensitivity symptoms are delayed, most typically appearing within 24 to 72 hours of eating the trigger food. This delay makes identification difficult without a structured assessment.

While not life-threatening, ongoing sensitivities can affect nutrition, disrupt the gut bacterial balance, and in some cases have been linked to autoimmune conditions. Common presentations include:

• Skin rashes, hives and eczema
• Fatigue and general weakness
• Brain fog and mood changes
• Cognitive & behavioural symptoms
• Achy joints and diffuse pain
• Bloating and irregular bowel movements

Food intolerance symptoms

Food intolerance symptoms are predominantly digestive, though they can extend beyond the gut.

Digestive:

• Loose stools through to watery diarrhoea (which may be smelly, frothy or contain mucus)
• Constipation
• Nausea, vomiting
• Flatulence, colic, abdominal pain

Other:

• Headaches and migraines
• Brain fog
• Eczema and hives
• Joint pain

What causes food allergies, sensitivities and intolerances?

The causes differ depending on the type of reaction, though several contributing factors can apply across all three.

Food allergies

True food allergies involve the immune system producing IgE antibodies against a food protein. On re-exposure, these antibodies trigger mast cells to release histamine, producing rapid and sometimes severe symptoms. Contributing factors include:

• Genetic predisposition to allergy
• A family history of allergic conditions – asthma, eczema or hay fever
• Skin exposure to a substance, particularly through broken or damaged skin
• Repeated occupational exposure (latex sensitisation, which commonly co-occurs with banana allergy, is a well-recognised example)

Alpha-gal allergy, triggered by certain tick bites, is a notable exception, producing an immune-mediated reaction to red meat and some animal products, including gelatin.

Food sensitivities

Food sensitivities involve a different part of the immune system. Instead of IgE antibodies, the body produces IgG antibodies, along with inflammatory signals that develop more slowly. Several things can contribute to this:

• Intestinal hyperpermeability (sometimes called leaky gut), where the gut lining becomes less effective at controlling what passes into the bloodstream, allowing food particles to trigger immune responses
• Gut flora imbalance, particularly reduced microbial diversity or an overgrowth of harmful species
• Impaired gastric or pancreatic secretions, meaning food is less thoroughly broken down before reaching the small intestine
• Reduced secretory IgA – an antibody produced in the gut lining that helps regulate what the immune system reacts to
• Reduced mucous production in the gut lining, which weakens the protective layer between digested food and the immune system
• Slow gut movement, which means food stays in contact with the gut lining for longer than it should
• Certain medications
• Frequently eaten foods, which can increase immune exposure

Food intolerances

Food intolerances most commonly result from an enzyme deficiency or an inability to process specific food compounds. Common triggers include:

• Lactose (lacking the enzyme lactase to digest milk sugar)
• Casein (milk protein)
• FODMAPs, salicylates, amines, sulphites, MSG and caffeine
• Wheat, yeast, corn, egg and certain legumes
• Poor fat digestion, often when the body isn’t producing enough bile
• Trehalose, a sugar found in mushrooms (the body needs a specific enzyme, trehalase, to digest it)

Persistent food reactions across all categories have been associated with a range of autoimmune and rheumatic conditions. The relationship is complex and not fully understood, but it reinforces why accurate identification and ongoing management matter.

How are food reactions investigated and assessed?

Assessment begins with a detailed clinical history. The type of symptoms, their timing relative to meals, which foods appear involved, and any relevant family or personal history all help to differentiate between allergy, sensitivity and intolerance before testing begins.

Standard allergy testing is helpful and includes:

• Skin prick testing for immediate (IgE-mediated) allergic reactions
• Specific IgE blood tests
• Oral allergen challenge, conducted under clinical supervision
• Patch testing for delayed contact-type reactions

These approaches are well-validated for true food allergies and are the standard of care in conventional medicine. Where a severe allergic reaction is possible, an adrenaline autoinjector (EpiPen) may be prescribed. Conventional management typically also includes antihistamines, corticosteroid sprays, or immunotherapy (a process of gradual desensitisation through repeated low-level allergen exposure over three to five years).

Functional testing extends further, particularly where sensitivities or intolerances are suspected:

• IgG and IgE food panel testing (such as the Precision Point P88 Dietary Antigen Test)
• Comprehensive microbiome testing to assess species diversity, inflammation markers, parasites and digestive function
• SIBO breath testing for bacterial overgrowth
• Assessment of gut barrier integrity and motility

Food diaries, elimination protocols and supervised reintroduction remain clinically valuable, particularly when laboratory findings are inconclusive or need contextual interpretation. Test quality and practitioner interpretation both matter significantly in this area. Due to variability in test quality, it is important to work with a practitioner who can access quality laboratories and is experienced in interpreting functional food sensitivity testing.

Why food reactions can persist after treatment

Conventional management of food allergies and intolerances typically focuses on avoidance. Avoidance removes the symptom trigger, but it does not address the conditions in the gut and immune system that may have allowed the reaction to develop in the first place.

For true IgE-mediated allergies, lifetime avoidance or immunotherapy is the primary approach. Immunotherapy gradually desensitises the immune system but does not resolve the underlying immune sensitivity that maintains the allergic tendency.

For food sensitivities, the picture is more complex and very common in our patient cohort. A permeable gut lining allows food proteins to pass into the bloodstream, provoking an immune response. If that permeability is not corrected, the immune system keeps encountering particles it identifies as threats, even after trigger foods are removed, and new sensitivities can develop for the same reason.

If gut flora imbalances, impaired digestive secretions or motility problems remain unaddressed, the conditions that created the sensitivity are still present. Removing a food may reduce symptoms, but reintroducing it, or introducing another problematic food, often provokes the same pattern of reactivity due to the residual antigen complexes that can take some time to break down.

For intolerances related to an enzyme deficiency, avoidance or enzyme support are the practical approaches. Where an intolerance is caused by gut dysfunction rather than a permanent enzyme absence, addressing those factors can substantially reduce reactivity. In these cases, the intolerance may improve substantially as gut function is restored.

In some people, food reactivity may extend beyond the gut-immune patterns described above. A pattern increasingly recognised in clinical practice is mast cell activation syndrome (MCAS), where mast cells release a wider range of inflammatory mediators beyond histamine in response to multiple triggers, not just food. A 2024 review in the Journal of Allergy and Clinical Immunology confirms this as a distinct condition that requires its own assessment, separate from standard food sensitivity investigation.

A functional medicine approach to food allergies, intolerances and sensitivities

A functional medicine approach looks beyond which foods are triggering reactions to understand why the immune system or digestive system is responding the way it is. Assessment typically looks at gut barrier integrity, digestive function, microbiome health, immune activity, and nutritional status.

Depending on your presentation, treatment may include:

• Dietary change: trigger foods may be removed short-term, but the focus is on supporting recovery rather than restriction – building the diet around foods that help repair the gut lining and restore a healthier bacterial environment
• Gut lining repair: where the gut lining has become more permeable than it should be, nutrients such as zinc and glutamine and herbs including slippery elm and meadowsweet may be used to support repair
• Microbial support: where testing identifies harmful bacteria or parasites, these are addressed before probiotic and prebiotic support is introduced to help restore bacterial diversity
• Digestive support: where stomach acid or enzyme output is low, digestive herbs such as gentian and ginger may be used to improve how food is broken down before it reaches the gut
• Immune support: where the immune system has become over-responsive to food, herbs including garlic, ginger, slippery elm, astragalus, and marshmallow may help bring reactivity back to a more appropriate level
• Anti-inflammatory and histamine support: herbs such as turmeric and boswellia may be used where inflammation is contributing to reactions; quercetin and related nutrients may help where histamine is involved
• Nutritional support: vitamin D, vitamin C, B vitamins, magnesium, and N-acetyl cysteine are commonly depleted in people with ongoing food reactions and may be recommended where deficiencies are identified

When to seek support

See your GP or a practitioner if you have:

• A pattern of reactions to food with no identifiable trigger
• Ongoing reliance on avoidance alone, without improvement
• Symptoms extend beyond the gut, including fatigue, skin reactions, brain fog or joint pain
• A family history of allergy or autoimmune conditions, alongside new or developing symptoms

Frequently asked questions

What is the difference between a food intolerance and a food sensitivity?

Food intolerance and food sensitivity are distinct reactions with different mechanisms. Food intolerance occurs when the body lacks the enzyme needed to break down a specific food, producing symptoms that are predominantly digestive and often dose-dependent. Food sensitivity involves an IgG immune response that can produce a wider range of symptoms across multiple body systems, and because the reaction is delayed, it is generally harder to identify without structured assessment.

How is a food sensitivity different from a food allergy?

A food sensitivity and a food allergy both involve the immune system producing symptoms on very different timescales. A true food allergy triggers IgE antibodies and produces symptoms within minutes to an hour, with the potential for anaphylaxis in severe cases. A food sensitivity involves IgG antibodies and produces a slower response, typically within 24 to 72 hours of eating the trigger food, which is what makes self-identification so difficult. Food sensitivities are not life-threatening in the way IgE allergies can be, but they can cause significant and wide-ranging symptoms when the trigger food is consumed regularly.

Can food sensitivities cause symptoms beyond the digestive system?

Yes. Because delayed food sensitivities involve immune activation rather than local gut irritation, the inflammatory response can extend throughout the body. Brain fog, fatigue, joint pain, skin rashes and mood changes are all recognised presentations, and ongoing reactivity can affect how the body regulates energy, mood and cognition.

Why do I react to more foods now than I used to?

Broadening food reactivity is usually a sign that something in the gut environment has changed, rather than individual foods becoming newly problematic in isolation. When the gut lining becomes more permeable, food particles pass into circulation and trigger immune responses more readily, and a disrupted microbiome makes this worse by reducing the immune system’s ability to tolerate food. Addressing the gut environment, rather than simply removing more foods, tends to reduce the overall breadth of reactivity.

How do I find out which foods I am sensitive to?

Identifying food sensitivities typically involves a combination of structured elimination, symptom tracking and targeted testing. Because reactions can be delayed by up to 72 hours, connecting symptoms to a specific food is rarely straightforward without a methodical approach. IgG food panel testing can identify likely immune triggers, though results are most useful when interpreted alongside a full symptom picture by a practitioner experienced in this area, as test quality in this field varies considerably.

How long does a food sensitivity reaction last?

A food sensitivity reaction can last anywhere from a few hours to several days, depending on the food involved, the degree of sensitivity, and the overall state of the gut and immune system. Because the reaction is immune-mediated, it does not resolve as quickly as a simple enzyme-based intolerance response might. Repeated exposure before a reaction has fully cleared can compound and extend symptoms, which is one reason ongoing reactivity is often difficult to trace back to a specific meal.

Can hormonal changes affect food reactions?

Yes. Hormonal changes, particularly during perimenopause and menopause, can directly influence food reactions. Oestrogen influences histamine release from immune mast cells, while progesterone acts as an anti-inflammatory buffer. As progesterone declines, that protective effect is reduced, and as both hormones fluctuate, histamine-related food reactions can become more pronounced, and existing intolerances may worsen noticeably without any obvious change in diet.

Can food intolerances be reversed?

Whether a food intolerance can be reversed depends on its underlying cause. Where it reflects a fixed enzyme deficiency, managing through avoidance or enzyme support is the practical approach. Where an intolerance is caused by gut dysfunction, such as intestinal hyperpermeability, flora imbalance, or impaired digestive secretions, addressing those factors can reduce reactivity substantially. In these cases, the intolerance is better understood as a consequence of a disrupted gut environment than a permanent fixed condition, and it can improve as that environment is restored.