The Gluten Free Society recently published the results of research on 247 recurrent canker sore sufferers and found strong suggestions of a link to gluten intolerance. From their post:
"canker sores can be associated with conditions that affect the GI tract, immune defects and syndromes that are inflammatory. They are not infectious or contagious in any way. However; up to 20% of patients with RAS are deficient in iron, vitamin B and folic acid. Another 3% have malabsorption or GI disorders. The detergent sodium lauryl sulphate found in toothpastes may aggravate them. And NSAIDs and other drugs can cause them."
The full article can be found here: http://www.glutenfreesociety.org/gluten-free-society-blog/canker-sores-a-sign-of-gluten-sensitivity/