Organization of microenvironments through which lymphocytes migrate is crucial for the generation of optimal immune responses and development [1]. In peripheral lymphoid organs, chemokines secreted by stromal cells are required for the constitution of T and B cell areas [2]. In the thymus, immature thymocytes attach to fibronectin via of α5β1 integrins [3]. Then, upon ligation of the preTCR, they upregulate CCR9 which triggers their attraction towards TECK-producing epithelial cells in the cortex and the medulla [4, 5]. Positively selected thymocytes lose CCR9 and acquire CCR4 and 7 which condition their migration towards chemokine gradient secreted by medullary stromal cells [6]. In re1Bdeficient mice, there is a complete disorganization of the cortico-medullary structure associated with a poor negative selection process [7–9]. These mice lack activated epithelial and myeloid-derived dendritic cells and, consequently, the expression of costimulatory or MHC molecules and the secretion of the medullary chemokine TCA4 are very low [10]. This animal model provides thus a useful link between the organization of a functional niche for negative selection and the activation of stromal cells. Using a panel of mAb directed at various types of stromal cells, we have found that the reactivity of some mAb was severely reduced in re1B-deficient thymuses. One of them was found to recognize the 106/JAM molecule, a novel member of the IgSF highly expressed by endothelial cells and most MHC class II-expressing stromal cells in thymus and peripheral lymphoid organs [11]. This molecule plays a stabilizing role in the formation of tight junctions [12] and is acquired upon tissue colonization by macrophages and dendritic cells. In this report, we describe the molecular cloning of the Ep-CAM molecules identified by the mAb 29 [8] used to define relB-dependent thymic medullary stromal cells in normal and autoimmune-prone animals.