Thymopoiesis is initiated by the colonisation of the epithelial rudiment with blood-borne hemopoietic precursors. Their subsequent differentiation to the functionally mature T cell subsets is exquisitely linked to sequential interaction with a diverse array of thymic epithelial cells which form discrete microenvironments. The development and organisation of the epithelium, however, is in turn controlled by thymocyte subsets. In particular the medulla organization depends upon activating signals provided by mature thymocytes to epithelial and dendritic cells. These signals are lacking in RelB-deficient mice leading to the disorganization of the corticomedullary junction and abnormal negative selection despite normal thymocyte maturation. This thymic stromal cell architecture phenotype is found in autoimmune diseases suggesting that abnormalities in the establishment of medullary microenvironments might be linked to the development of autoimmunity.