Thymoma is frequently associated with autoimmune diseases, including myasthenia gravis (MG). The failure of thymoma microenvironment to induce T cell tolerance may be responsible for its association of MG. Autoimmune regulator (AIRE) expression in the medullary thymic epithelial cells has been reported to play a role in presenting autoantigen and induction of tolerance. We studied AIRE mRNA in 45 thymomas and three normal thymi using quantitative reverse transcription polymerase chain reaction (RT-PCR). Only 23/45 (51.1%) of thymomas expressed AIRE mRNA at low levels while all normal thymi expressed AIRE mRNA. There was no correlation between AIRE mRNA and association of MG or presence of anti-acetylcholine receptor antibody. The infrequent and low expression of AIRE mRNA may play a role the induction of autoimmune diseases but other factors also seem to be involved.