One prediction from the complex series of steps in intrathymic T-cell differentiation is that to regulate it the stroma controlling the process must be equally complex: the attraction of precursors, commitment to the T-cell lineage, induction of T-cell receptor (TCR) gene rearrangement, accessory molecule expression, repertoire expansion, major histocompatibility complex (MHC) molecule-based selection (positive and negative), acquisition of functional maturity and migratory capacity must all be controlled. In this review, Richard Boyd and Patrice Hugo combine knowledge of T-cell differentiation with thymic stromal cell heterogeneity to offer an integrated view of thymopoiesis within the thymic microenvironment.