Aphthous ulcers, commonly called canker sores, result from an overactive immune response that destroys small patches of the tissue lining your mouth. No single cause has been identified, but the process involves a combination of immune dysfunction, nutritional gaps, stress, genetics, and environmental triggers that vary from person to person. Understanding which factors are at play can help you reduce how often these painful sores return.
How the Immune System Attacks Oral Tissue
The core event behind an aphthous ulcer is your own immune cells turning against the lining of your mouth. Certain white blood cells, particularly a subset called gamma-delta T cells, are found in higher numbers in people with active ulcers. These cells drive a process called antibody-dependent cytotoxicity, essentially marking healthy tissue for destruction. Once the attack begins, the body releases signaling molecules that sustain inflammation and recruit even more immune cells to the area, deepening the damage.
People prone to canker sores also show elevated blood levels of several inflammatory markers, including molecules that help immune cells stick to and penetrate blood vessel walls. A key part of the problem appears to involve a misfiring in one of the body’s early-warning immune pathways, which triggers an exaggerated inflammatory response instead of a measured one. This is why aphthous ulcers aren’t infections. They’re the result of your immune system overreacting, often to triggers that wouldn’t bother most people.
Nutritional Deficiencies
Low levels of certain vitamins and minerals are one of the most well-documented contributors to recurrent canker sores. The three most common deficiencies are vitamin B12, folate, and iron. In one case-control study of 40 people with recurrent aphthous ulcers, 75% had deficiencies in B12 or folate. These nutrients are essential for healthy cell turnover in the mouth lining, which replaces itself roughly every one to two weeks. When the raw materials for that process are missing, the tissue becomes more fragile and more susceptible to immune-mediated breakdown.
If you get canker sores frequently, it’s worth having your levels checked through a simple blood test. Correcting a deficiency through diet or supplementation often reduces the frequency and severity of outbreaks. Good dietary sources of these nutrients include leafy greens, legumes, eggs, red meat, and fortified cereals.
Stress and Cortisol
Stress is one of the most commonly reported triggers, and the biological evidence supports it. A study of 69 people measured salivary cortisol (the body’s primary stress hormone) and salivary alpha-amylase (a stress-responsive enzyme) in patients with active ulcers, patients in a post-healing phase, and healthy controls. Both stress markers were significantly elevated in ulcer patients compared to controls, not just during active outbreaks but also after the sores had healed.
That lingering elevation in stress hormones even after healing suggests that people who get frequent canker sores may live with chronic, low-grade stress or anxiety that keeps their immune system primed for overreaction. Cortisol in short bursts suppresses inflammation, but chronic elevation can paradoxically dysregulate the immune system, making inflammatory flare-ups more likely. This helps explain why ulcers so often coincide with exam periods, work deadlines, or emotionally difficult stretches of life.
Changes in Oral Bacteria and Fungi
The community of microbes living in your mouth shifts noticeably during active ulcers. In people with canker sores, researchers have found increases in several opportunistic bacteria that are normally kept in check, along with decreases in protective species that help maintain a balanced oral environment. One study identified two bacterial species as most closely linked to aphthous ulcers, with the most dramatic microbial changes occurring on the inner surface of the lower lip.
Fungal shifts matter too. During active outbreaks, a yeast called Malassezia tends to dominate, followed by Candida. These organisms appear to have a negative relationship with some of the protective bacteria that decline during ulceration. It’s not yet clear whether these microbial changes help cause the ulcer or simply take advantage of damaged tissue, but the pattern is consistent enough that oral microbiome disruption is considered part of the picture.
Toothpaste and Other Irritants
One of the most actionable findings in aphthous ulcer research involves sodium lauryl sulfate (SLS), a foaming agent found in most commercial toothpastes. In a study of 10 patients with frequent canker sores, switching from an SLS-containing toothpaste to an SLS-free version for three months reduced ulcer count by about 64%, dropping from an average of 14.3 ulcers to 5.1 over the same period. The reduction compared to their baseline (before the study, using their regular toothpaste) was about 70%.
SLS is thought to strip away the protective mucous layer in the mouth, leaving tissue more vulnerable to damage and immune attack. If you deal with frequent canker sores, switching to an SLS-free toothpaste is one of the simplest changes you can make. Several widely available brands market themselves as SLS-free, so check the ingredient list on the back of the tube.
Physical trauma also plays a role. Biting your cheek, aggressive brushing, sharp edges on dental work, or even hard food can create a small wound that the immune system then amplifies into a full ulcer in susceptible people.
Food Triggers
Many people notice that certain foods seem to set off canker sores, with citrus fruits, tomatoes, spicy foods, and chocolate among the most commonly reported culprits. However, this does not appear to be a true food allergy. The American Academy of Allergy, Asthma, and Immunology notes there is no evidence that immunologic food reactions are responsible for aphthous ulcers. What likely happens is that acidic or abrasive foods irritate already-vulnerable tissue, lowering the threshold for an ulcer to develop. Some people may also have individual sensitivities to certain food components that trigger inflammation through non-allergic pathways.
Underlying Medical Conditions
Recurrent canker sores can sometimes be a sign of a broader health issue. Several systemic conditions are known to produce oral ulcers that look identical to ordinary aphthous sores, and these should be considered when ulcers are unusually frequent, severe, or slow to heal.
- Celiac disease causes intestinal damage from gluten and frequently shows up as oral ulcers, sometimes before any digestive symptoms appear.
- Crohn’s disease produces inflammation anywhere in the digestive tract, including the mouth.
- Behçet’s syndrome is an inflammatory condition that causes ulcers in the mouth and genitals, along with eye inflammation.
- HIV and other immunodeficiencies can increase ulcer frequency and severity.
- PFAPA syndrome in children causes recurring episodes of fever, sore throat, swollen lymph nodes, and mouth ulcers on a predictable cycle.
If your ulcers are accompanied by other symptoms like chronic digestive problems, joint pain, genital sores, or recurring fevers, the ulcers may be pointing toward one of these conditions rather than standalone aphthous stomatitis.
Genetics and Family History
Canker sores run in families. If both your parents get them, your risk is significantly higher. Researchers have investigated whether specific genetic markers, particularly certain immune-system genes called HLA types, explain this hereditary pattern. One Korean study found that the genetic marker HLA-B51, strongly associated with Behçet’s syndrome, appeared in only 16.1% of people with recurrent aphthous ulcers, virtually the same as the 15.7% rate in healthy controls. This suggests that while canker sores clearly have a genetic component, it’s likely spread across multiple genes rather than tied to a single identifiable marker. The hereditary influence probably affects how your immune system is calibrated, how quickly your oral tissue heals, and how strongly you respond to environmental triggers.
The Three Types of Aphthous Ulcers
Not all canker sores are equal. They fall into three categories that differ in size, severity, and how long they stick around.
Minor aphthous ulcers account for the vast majority of cases. They’re typically 2 to 3 millimeters across, always under 8 mm, and heal within about 10 days without scarring. These are the small, round sores most people picture when they think of a canker sore.
Major aphthous ulcers are deeper and larger than 1 centimeter. They can last weeks to months and often leave scars. These are significantly more painful and can interfere with eating and speaking.
Herpetiform aphthous ulcers (named for their appearance, not the herpes virus) begin as clusters of up to 100 tiny sores that merge into larger irregular ulcers. Despite the alarming number, they typically resolve within about two weeks. They’re the least common of the three types.