Canker sores are caused by an overactive immune response that destroys small patches of tissue inside your mouth. Unlike cold sores, which are viral infections, canker sores are not contagious and form only on the soft tissues inside the mouth: the inner cheeks, lips, tongue, and gums. The exact trigger varies from person to person, but the underlying process involves your own immune cells attacking the thin lining of your mouth.
The Immune Response Behind the Sore
At the cellular level, canker sores form when certain white blood cells, specifically T cells, begin destroying the delicate tissue that lines the inside of your mouth. These immune cells release inflammatory signaling molecules that attract even more immune activity to the area, creating a cycle of tissue damage. People who get frequent canker sores have higher blood levels of several of these inflammatory signals, suggesting their immune system is essentially on a hair trigger when it comes to oral tissue.
One theory is that this response is a case of mistaken identity. A common mouth bacterium shares structural similarities with proteins found in your own cells. Your immune system may mount an attack against the bacterium and accidentally damage healthy tissue in the process. This helps explain why canker sores tend to appear at sites of minor trauma, where bacteria can more easily contact exposed tissue and kick off this misguided immune reaction.
Common Triggers
While the immune system does the actual damage, several everyday factors can set the process in motion:
- Physical injury: Biting your cheek, aggressive brushing, dental work, or braces rubbing against tissue are among the most common triggers. Even eating sharp or crunchy foods can scratch the lining enough to start a sore.
- Stress and sleep deprivation: Emotional or physical stress alters immune function and is one of the most frequently reported triggers in people who get recurring sores.
- Hormonal shifts: Many women notice sores appearing at specific points in their menstrual cycle, suggesting hormone fluctuations play a role.
- Certain foods: Acidic fruits (citrus, tomatoes, strawberries), spicy foods, and chocolate are well-known irritants for susceptible people.
- Nutritional deficiencies: Low levels of iron, zinc, folate, or vitamin B12 are linked to more frequent outbreaks.
Your Toothpaste May Be a Factor
One of the more surprising and actionable causes is sodium lauryl sulfate (SLS), a foaming agent found in most commercial toothpastes. A systematic review published through the American Dental Association found that people who switched to SLS-free toothpaste developed significantly fewer ulcers, experienced shorter healing times, had fewer recurring episodes, and reported less pain. Across the studies reviewed, SLS-free toothpaste users averaged roughly one fewer active ulcer at any given time compared to those using standard toothpaste.
SLS strips away the protective mucous layer inside your mouth, making the tissue more vulnerable to irritation and the kind of minor damage that can trigger an immune response. If you get canker sores regularly, switching to an SLS-free toothpaste is one of the simplest changes you can make. Several brands market themselves as SLS-free, and you can confirm by checking the ingredient list on the back of the tube.
Genetics and Family History
If your parents get canker sores, you’re more likely to get them too. Research has identified specific immune-related genes (part of the HLA system, which helps your body distinguish its own cells from invaders) that are associated with higher susceptibility. Certain variants of these genes, particularly HLA-DRB1*0401 and HLA-Cw*0303, appear more frequently in people with recurrent canker sores. Conversely, other HLA variants seem to offer protection, appearing significantly more often in people who rarely or never develop them.
This genetic component helps explain why some people can bite their cheek, eat a bag of oranges, and brush with any toothpaste without ever developing a sore, while others seem to get one from the slightest provocation.
Underlying Health Conditions
Frequent, severe canker sores can sometimes signal a systemic health issue. Celiac disease is one of the strongest associations. People with celiac disease experience more frequent and more severe outbreaks of canker sores, and in some cases, recurring mouth ulcers are one of the first noticeable symptoms before the condition is formally diagnosed. A gluten-free diet often reduces or eliminates the sores in these patients.
Other conditions linked to recurrent canker sores include Crohn’s disease and ulcerative colitis (both inflammatory bowel diseases), Behçet’s disease (an inflammatory condition that causes ulcers in multiple parts of the body), and immune deficiencies including HIV. In people with weakened immune systems, canker sores can take months to heal rather than the typical one to two weeks. If your sores are unusually large, appear in clusters, or refuse to heal, that pattern is worth bringing up with a healthcare provider.
Three Types of Canker Sores
Not all canker sores look the same. Minor aphthous ulcers are the most common type, measuring less than 1 centimeter across. They’re shallow, white or yellowish with a red border, and typically heal on their own within one to two weeks without scarring.
Major aphthous ulcers are larger and penetrate deeper into the tissue. These are significantly more painful, can take weeks or even months to heal, and sometimes leave scars. Herpetiform ulcers (named for their appearance, not the herpes virus) show up as clusters of many tiny sores that may merge into larger irregular shapes. Despite their name, they are not caused by a virus and are not contagious.
Canker Sores vs. Cold Sores
These two conditions are commonly confused, but the easiest way to tell them apart is location. Canker sores form only inside the mouth, on soft tissues like the inner cheeks, lips, tongue, or gums. Cold sores (fever blisters) form on the outside of the mouth, typically around the border of the lips. Cold sores are caused by the herpes simplex virus and are highly contagious, while canker sores are an immune reaction with no viral cause and cannot spread to other people.
Cold sores also look different: they start as fluid-filled blisters that eventually crust over. Canker sores are open, shallow ulcers from the start, appearing as white or yellow patches surrounded by redness.
Treatment Options That Help
Most minor canker sores heal without any treatment in one to two weeks. The goal of treatment is to reduce pain, speed healing, and prevent secondary infection. Over-the-counter options include topical numbing gels containing benzocaine and antiseptic mouth rinses. Coating products that form a protective barrier over the sore can also reduce pain from eating and drinking.
For more persistent or painful sores, prescription-strength topical corticosteroid pastes can reduce inflammation and shorten healing time. These are applied directly to the sore several times a day. Salt water or baking soda rinses (about half a teaspoon in a cup of warm water) can also soothe irritation and help keep the area clean.
Avoiding irritating foods while a sore is active makes a practical difference. Acidic, spicy, and rough-textured foods all increase pain and can slow healing. Soft, cool, or room-temperature foods are easier to tolerate. For people who get recurring sores, addressing the underlying triggers (switching toothpaste, managing stress, correcting nutritional deficiencies, or screening for conditions like celiac disease) is more effective than treating each individual sore as it appears.