A Recurrent Apthous Ulcer, frequently referred to as a "Canker Sore"  is similar to any ulcer in that it is an area where the outer layer of mucosa (lining of the inside of the mouth) is gone.  This leaves the tissue underneath bare with nerve endings exposed.  Since the integrity of the mucosa is broken,  bacteria invade, and the result is inflammation which makes the ulcer even more painful.  The inflammation in and around a tiny mouth ulcer can cause big pain, especially if it is on a place that is frequently used (e.g., tip of the tongue, inside of the lower lip.)
 
Apthous ulcers start as little red bumps and they develop into a characteristic central spot of denuded mucosa surrounded by a bright red ring area of inflammation. Once they start, they run their course, which usually means that over the next ten days or so,  they get larger and more sore before they become covered with a grayish coating and heal.  They often occur in waves and are a frequent problem for some.

Apthous ulcers (unlike Herpes ulcers)  occur on "unattached" gum or mucosa.  That means the area of tissue where they are found will not be attached to the underlying bone. They will be seen on free, moveable tissue, like the inside of cheeks and lips, on the tongue, or on the soft palate and throat. (The soft palate is behind the hard palate (way back there) including the uvula (the gagging piece that hangs down). Recurrent apthous ulcers do not occur on the hard palate but they do occur right behind the hard palate, way back on the roof of the mouth.  These can hurt when swallowing, making the patient think he or she has a cold.

It seems clear that apthous ulcers are not caused by a virus, as are the Herpes ulcers.  Most probably the cause is this:  Bacteria (probably a strep) enter some mucosal cells.  The body responds with an autoimmune reaction to the infected skin, attacking it.  This scenario seems to happen more easily when mucosa is thin (e.g., in the low estrogen phase of the menstrual cycle or at menopause in women) or when mucosa is irritated or scratched.  I have seen strep infections in which every little red infected spot on the mouth was followed by an apthous ulcer formation. 

Prevention: For those who get frequent canker sores/ulcers, there is a prevention program that works:  The patient rinses routinely with an antibacterial chlorhexidine  mouthwash such as Peridex, either once or twice a day. This keeps bacteria from attacking the mucosa.  Then,  if an ulcer or canker sore starts to develop,  the patient also starts to rinse with Dexamethasone containing mouthwash a couple times a day.  This is a low dose topical steroid that suppresses the autoimmune response.  Prescriptions are needed for both these items.  As a long time sufferer of canker sores, though,  I can tell you that this is my first recommendation to patients. If you have frequent recurrent apthous ulcers it is worth discussing this with your physician or dentist.  Having these two bottles of mouthrinse handy can save a lot of pain.

If a canker sore has already developed, these two rinses will still give some real relief.Peridex keeps the sore area from becoming overgrown with bacteria,  and with fewer bacteria, there will be less inflammation and pain. Dexamethasone reduces painful inflammation and halts the autoimmune response. The both are used in the development of the ulcer the more effective they will be.

Aspirin or Ibuprofen can be taken for the pain as well (not placed on the ulcer but swallowed with a glass of water).   Various numbing ointments, or pastes meant to cover the ulcer  may help,  and some swear by the amino acid Lysine used topically.