Ever notice how canker sores show up at the worst times? Right after you have been sick. A few days after a vaccine. During finals week or a stressful stretch at work.
There are a lot of theories about what causes canker sores. The one that best fits the pattern (and shows up repeatedly in the research literature) is this: for many people, canker sores look like an immune reaction that hits the wrong target.
If you are new here and want the basics first, start with: What Is a Canker Sore?
The short version
- Canker sores are not contagious. They are usually framed as an inflammatory or immune-mediated ulcer, not an infection you “catch.”
- A common model is immune “friendly fire”: immune cells (especially T cells) show up and damage the mouth lining.
- Immune activation can be a trigger: illness, stress, and sometimes vaccines can coincide with outbreaks for some people.
- The prevention playbook is mostly about reducing misfires: fix nutritional gaps, avoid mouth trauma, consider SLS-free toothpaste, and manage stress where possible.
Important (Medical disclaimer)
This article is informational only. If your ulcers are severe, persistent, unusually frequent, or come with systemic symptoms, talk to a clinician.
The “friendly fire” idea
Think of the immune system like a security team. Most of the time, it identifies real threats (viruses, bacteria) and clears them. Sometimes it makes a mistake. It treats the tissue lining your mouth as the problem.
When researchers look at active canker sores under a microscope, they often find a large immune-cell infiltrate, including a lot of T cells, consistent with an immune-driven injury pattern. A review-style overview is here: StatPearls: Recurrent Aphthous Stomatitis
This does not mean “autoimmune disease” in the formal diagnosis sense for everyone. It means that the mechanism of damage in many sores looks immune-mediated.
What happens when a sore forms (step by step)
This is a practical way to picture the sequence:
- A trigger primes the area: stress, a minor injury (biting your cheek), illness, dental work, or sometimes a medication change.
- Immune cells accumulate locally: you might feel a tingle, burning, or tenderness before anything is visible.
- Inflammatory signals ramp up: cytokines act like “alarm” molecules that amplify the response.
- The surface breaks down: the top layer erodes, leaving the familiar white or yellow crater with a red border.
Even if the trigger is different person to person, the end result can look similar: localized inflammation and tissue breakdown.
The signaling molecules people talk about (cytokines)
Many papers discuss cytokines in recurrent aphthous stomatitis. You will commonly see TNF-alpha, interleukins, and interferon-gamma mentioned.
Here is the simplified takeaway: a higher inflammatory tone can make sores more likely, more painful, or slower to heal.
| Signal | What it generally does | Often reported in RAS literature |
|---|---|---|
| TNF-alpha | Amplifies inflammation and tissue damage signaling | Elevated in some studies |
| IL-2 | Promotes T cell activation and expansion | Elevated in some studies |
| Interferon-gamma | Activates immune killing pathways | Elevated in some studies |
If you want a deeper immunology review angle, this open-access overview is a starting point: The Immune System and Recurrent Aphthous Stomatitis (review)
Vaccines, illness, and “why did this happen right now?”
People report outbreaks after illness and sometimes after vaccines. Two things can be true at once:
- Vaccines and infections activate the immune system on purpose.
- An activated immune system can sometimes overshoot, especially if you are already susceptible, stressed, or dealing with other triggers (like mouth trauma).
Importantly, this is not an argument against vaccination. It is a way to explain timing if you notice a pattern.
If you want an epidemiology-style look at oral adverse events after COVID-19 vaccination, one paper that discusses reported events (including mouth ulcers) is here: Frontiers: Oral adverse events following COVID-19 vaccination (VAERS-based analysis)
What you can do to reduce outbreaks (practical and testable levers)
This is the part that matters if you are trying to get fewer sores, not just a better explanation.
1. Fix nutritional gaps (especially the ones linked in the literature)
Nutritional deficiencies do not explain every case, but they are one of the few areas that are both testable and fixable.
Commonly discussed nutrients include:
| Nutrient | Why it might matter | Notes |
|---|---|---|
| Vitamin B12 | Supports mucosal health and cell turnover | There is RCT evidence for daily B12 reducing outbreaks in some people |
| Folate | Tissue repair and cell division | Often paired with B12 in workups |
| Iron | Oxygen delivery and tissue healing | Iron deficiency can show up with oral symptoms |
| Zinc | Immune function and wound healing | Sometimes low in frequent-ulcer groups |
If you want a deeper, evidence-first guide specifically on B vitamins, see: Not All the Bs Are the Same: Vitamin B and Canker Sores
2. Avoid “mouth trauma” during high-risk windows
Small injuries can be enough to start the process. During stressful weeks, right after illness, or when you are run down, try to be extra careful with:
- cheek or lip biting
- sharp or crunchy foods
- aggressive brushing
- dental work timing (when you have flexibility)
3. Consider switching to SLS-free toothpaste
Sodium lauryl sulfate (SLS) is a foaming detergent that can irritate oral tissue in some people. For a subset of canker sore sufferers, switching helps.
Guide here: SLS-Free Toothpaste for Canker Sores: Does It Help?
4. Manage stress, even if you cannot eliminate it
Stress is not a satisfying answer, but it is a real association in many people’s timelines. If you already know your “canker season” lines up with sleep deprivation, deadlines, or travel, treat those periods like higher risk.
When to stop guessing and get evaluated
Talk to a clinician if ulcers are:
- lasting longer than 2 to 3 weeks
- unusually large
- happening very frequently
- accompanied by fever, weight loss, severe fatigue, or other systemic symptoms
Recurring mouth ulcers can overlap with conditions like celiac disease, inflammatory bowel disease, and other immune-mediated issues. If your pattern is extreme, it is worth a workup.
The bottom line
For many people, the best working explanation for canker sores is not “random bad luck.” It is an immune response that sometimes misfires, especially during periods of stress, illness, or local irritation.
The best prevention strategies tend to be the boring, high-signal ones:
- correct nutritional deficiencies (B12, folate, iron, zinc)
- remove common irritants (like SLS) if you are sensitive
- reduce mouth trauma
- protect sleep and stress where you can
Sources and further reading
- StatPearls: Recurrent Aphthous Stomatitis
- Review: The immune system and recurrent aphthous stomatitis (PMC)
- Nature Communications: Genetic study of 461,000+ people (RAS-associated loci)
- Frontiers: Oral adverse events following COVID-19 vaccination (VAERS-based analysis)
- Cleveland Clinic: Canker sore overview