Canker sores are caused by an overactive immune response that destroys small patches of tissue inside your mouth. Unlike cold sores, they aren’t caused by a virus and aren’t contagious. The exact reason your immune system turns on the oral lining varies from person to person, but the triggers fall into a handful of well-understood categories: physical injury, nutritional gaps, genetics, stress, hormonal shifts, and certain ingredients in toothpaste.
How the Immune System Creates the Ulcer
At the cellular level, a canker sore is an immune attack on your own tissue. Specific immune cells (a type of white blood cell called CD8+ T cells) target and destroy the thin layer of cells lining the inside of your mouth. The process is driven by an inflammatory signaling molecule called TNF-alpha, which recruits additional immune cells to the site and ramps up inflammation. Other inflammatory signals pile on, and the result is the painful, crater-like wound you see and feel.
This is why canker sores aren’t random damage. They’re a localized inflammatory event, which explains why they respond to anti-inflammatory treatments and why people with overactive immune systems tend to get them more often.
Physical Trauma to the Mouth
Biting your cheek, poking your gum with a chip, or burning the roof of your mouth with hot food can all set off the immune cascade that forms a canker sore. For some people, even minor friction is enough. Orthodontic braces are a well-documented trigger: brackets, wires, and bands rub against the soft tissue, breaking down the protective mucosal barrier and causing ulceration. Adjustments and wire tightening make it worse, and the sharp edges of brackets are frequent culprits.
Dental work, ill-fitting dentures, and aggressive tooth brushing can do the same thing. If you notice sores appearing at the exact spot where something rubs or pokes, the cause is almost certainly mechanical.
Nutritional Deficiencies
Low levels of iron, vitamin B12, or folate are a recognized cause of recurrent canker sores. Screening studies have found nutritional deficiencies in roughly 14 to 18 percent of people with recurring ulcers. These nutrients play key roles in maintaining the health of rapidly dividing cells like the ones lining your mouth. When levels drop, the tissue becomes more vulnerable to breakdown and slower to repair.
If you get canker sores frequently and can’t identify an obvious trigger, a blood test checking these three nutrients is a reasonable step. Correcting a deficiency often reduces how often sores return.
Toothpaste Ingredients
Sodium lauryl sulfate (SLS), a foaming agent in most commercial toothpastes, irritates the oral lining and is linked to more frequent canker sores. A systematic review of clinical studies found that switching to an SLS-free toothpaste significantly reduced the number of ulcers, the duration of each ulcer, the number of episodes, and the level of pain. SLS strips away the protective mucus layer inside the mouth, leaving the tissue more exposed to irritation and immune overreaction.
This is one of the easiest triggers to eliminate. SLS-free toothpastes are widely available, and many people who make the switch notice a clear improvement within a few weeks.
Genetics and Family History
Canker sores run in families, and research has identified specific genetic markers that appear more frequently in people who get them. Certain immune-system genes (part of the HLA system, which helps your body distinguish its own cells from invaders) show up at much higher rates in people with recurrent sores. In one study, a marker called HLA-B35 appeared in 48 percent of canker sore patients compared to 21 percent of healthy controls. Another marker, HLA-DR7, was found in 62 percent of patients versus 27 percent of controls.
Researchers have confirmed that susceptibility to canker sores is inherited along with these immune-system gene patterns, even though no single gene has been pinpointed as “the” canker sore gene. If one or both of your parents dealt with frequent canker sores, your chances of getting them are substantially higher.
Stress and Hormonal Changes
Emotional stress is one of the most commonly reported triggers, likely because stress hormones suppress some parts of the immune system while amplifying others, tipping the balance toward the kind of inflammatory response that produces ulcers. Many people notice sores appearing during exam periods, work deadlines, or emotionally difficult stretches.
Hormonal shifts also play a role for some women. Canker sores sometimes flare in sync with the menstrual cycle, coinciding with the rise in progesterone levels in the second half of the cycle. In rare cases, this represents an actual immune sensitivity to progesterone. Among documented cases of progesterone-related skin and mucosal reactions, the menstrual cycle was the predisposing factor 73 percent of the time. While a true progesterone allergy is uncommon, many women with recurrent sores notice a cyclical pattern worth tracking.
Underlying Health Conditions
Frequent, severe, or unusually persistent canker sores can be a sign of a systemic condition. Three diseases are most closely associated with recurrent oral ulcers:
- Celiac disease: The immune reaction to gluten damages the intestinal lining but also affects the mouth. Some people with celiac disease experience canker sores as one of their earliest or only symptoms, sometimes before any digestive issues appear.
- Crohn’s disease: This inflammatory bowel condition can cause ulceration anywhere along the digestive tract, including the mouth. Oral ulcers in Crohn’s disease tend to be deeper and slower to heal.
- Behçet’s disease: This is a systemic inflammatory disorder where recurrent oral ulcers are actually part of the diagnostic criteria. Diagnosis requires at least three episodes of oral ulcers within 12 months, plus additional symptoms such as genital ulcers, eye inflammation, or specific skin lesions.
If your canker sores are unusually large, take more than two weeks to heal, or come with symptoms outside the mouth, these conditions are worth investigating.
Oral Microbiome Shifts
The balance of bacteria in your mouth appears to shift during canker sore outbreaks. Research comparing the oral microbiomes of people with and without recurrent sores has found distinct bacterial profiles that differ between the two groups. Certain bacterial signatures are more common in patients who have an active ulcer at the time of testing, while other bacterial populations are reduced compared to healthy controls.
Earlier theories pointed to specific species like H. pylori or Streptococcus as culprits, but more recent analysis hasn’t confirmed those individual species as the key players. The picture looks more like a general shift in microbial balance rather than a single “canker sore germ.”
Three Types and How They Differ
Not all canker sores are the same size or severity. They fall into three categories, and knowing which type you’re dealing with helps set expectations for healing.
Minor canker sores are by far the most common. They measure 2 to 5 millimeters across (smaller than a pencil eraser), and they heal on their own within 4 to 14 days without scarring. Major canker sores are 1 to 3 centimeters in diameter, deeply set into the tissue, and can last anywhere from 10 days to 6 weeks or longer. These often leave scars. Herpetiform canker sores are tiny (1 to 2 millimeters) but appear in clusters, which can make them look like a herpes outbreak even though they have nothing to do with the herpes virus. They typically resolve within 7 to 10 days.
Most people who search for canker sore causes are dealing with the minor type. If yours regularly exceed a centimeter or take more than three weeks to heal, that pattern points toward one of the underlying conditions or deficiencies worth investigating further.