Canker sores are caused by a variety of sources.
The most common source is a tiny injury to the lining of the mouth (from braces, misaligned teeth, crunchy foods, dentistry, etc.)
Another likely cause is toothpaste containing a harsh chemical detergent called sodium lauryl sulfate (or SLS).
Food Allergies including allergies to milk and nuts are believed to trigger canker sores in some people.
Diets lacking B-vitamins, folic acid, and iron can be the culprit.
Many canker sores are worsened by the appearance of helicobacter pylori; this is the same organism that causes most stomach ulcers.
Switching to a natural toothpaste and non-alcoholic mild mouthwash help most people who suffer from these annoying ulcerations in the mouth.
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One thing you can do is rinse with mouth wash. It might sting for a little bit but its taking away the pain. You could rinse with salt water or even brush you teeth and brush over the sore. If it doesn't take it away right away then it should be gone by the next day, if not the pain should be taken away.
That can come from eating too much acidic food, like tomatoes. Cut back on such foods, keep your mouth rinsed out. Don't lick canker sores; that can brush bacteria into the sore, and make it worse. Powdered alum on the sore can speed healing; don't lick that either. (It tastes nasty.)