T-cell development in the thymus is a stepwise process, mediated by a variety of stromal cells in different regions of the organ. Although the cellular composition of the thymic microenvironment has been known for over a decade, the molecular cues that govern its formation are only beginning to be understood. Stromal-derived chemokines attract T-cell precursors to the thymus and direct maturing thymocytes to appropriate niches for their further development. Reciprocal signals from developing T cells provide crosstalk that is essential for establishment and maintenance of the thymic microenvironment. Elucidation of the molecular players involved and their context within the organ is the challenge for the field today. This knowledge could then be translated to clinical restoration of thymic function and T-cell reconstitution.