How do medications treat aphthous stomatitis (canker sore)?

Canker sores typically heal on their own within a week. For temporary relief, there are over-the-counter topical anesthetics and antimicrobial mouthwashes. Antibiotics from your dentist and some oral bandages can reduce secondary infection.

Several antibiotic medications (triamcinolone, fluocinonide, and amlexanox) may be used to treat especially painful canker sores (also known as aphthous stomatitis). Although the exact way in which the various drugs work is different, they all reduce the amount of inflammation in the area of the canker sore and allow the sore to heal. 

The advantage of using one of these medications is that they reduce pain, the main symptom of canker sores. The disadvantage is that, as with nearly all medications, you could end up with side effects from the drug. If you are unsure about whether you should take something for your painful canker sore, ask your doctor.  He or she may recommend a home-based treatment, or may suggest that a prescription antibiotic may be the better option for you.

In many cases, aphthous stomatitis (canker sore) does not require treatment with medications. The sore usually disappears within two weeks. However, topical over-the-counter (OTC) gel medications containing a pain killer may relieve pain and help speed healing. If aphthous stomatitis does not clear up on its own, a doctor may prescribe stronger medications or look for an underlying health condition.