Background:  The reduced ability to activate oral tolerance plays a role in the pathogenesis of some gastrointestinal inflammatory diseases. This activation may reflect a preferential reduction of a T‐helper (Th)2‐ or Th3‐type response. In recurrent aphthous ulceration (RAU), genetic and environmental factors may contribute to low tolerance, permitting a cytotoxic reaction against the oral epithelium. The cytokine profile has not permitted the definition of RAU as resulting from enhanced Th1 or Th2 responses. A cDNA microarray study would allow the identification of differentially expressed genes and provide a basis for classification of the immune response.

Methods:  The cDNA from 29 samples of aphthae and from 11 samples of normal mucosa from aphthae‐free volunteers were hybridized on microarray membranes with 1176 genes.

Results:  Forty‐one differentially expressed genes were identified, and a higher expression level of the Th1 gene cluster in RAU was found.

Conclusions:  Microarrays permitted us definition of the gene expression profile of the lesion and identify an increased Th1 activity in RAU lesions.