Canker sores are a painful part of life that many people have to deal with. In fact, they are the most common sores in the mouth experienced by people in the US. Unfortunately, we still don't completely understand what causes them, but it seems to have something to do with the balance and imbalance of the cells that fight infection, and the chemicals that control them. Things that make you more likely to have them often include stress, changes in hormone levels, illness
, and other people in your family that have them as well.
Treatment options are somewhat limited, mostly because they usually get better by themselves over just a week or two, and don't leave any scarring. If they are bothering you too much (as it sounds like yours are), you can try over the counter preparations that numb the area (something with benzocaine, for example) and others that treat the inflammatory cells that come to the area (such as Orabase). If these sores persist, have other symptoms than just the annoyance and pain, or start to affect your life in any other way, you should probably speak to your dentist
or primary care doctor