Autoimmune regulator (AIRE) is a transcription factor expressed in the thymic medullary epithelial cells (MECs). MECs have been suggested to contribute to tolerance induction by presenting tissue specific antigens to T cells that react to these antigens. AIRE expression in cells other than MECs has not been studied extensively. Here we report four-color flow cytometric and quantitative real-time PCR studies on the expression of AIRE in the lymphoid cells in the thymus and periphery. In the thymus AIRE was expressed in B cells and CD4+CD8+ double positive cells at a low level. In the peripheral blood AIRE was expressed in B cells but not in T cells, and also expressed in CD14+ dendritic cells (DCs)/macrophages and granulocytes at higher levels. AIRE mRNA was expressed higher in B cells than in T cells. Further study is warranted to define the functional role of the AIRE expressed in the lymphoid cells.