The epithelial component of the thymic environment is organized into discre
te cortical and medullary compartments that mediate different aspects of th
ymocyte differentiation. The processes controlling the growth and organizat
ion of these epithelial compartments are poorly defined. In this study we h
ave used a novel approach to define the three-dimensional organization of t
hymic epithelial (TE) compartments to demonstrate that the organization of
the medullary TE compartment is very complex. A spatial relationship of med
ullary thymic epithelium with vascular elements of the thymus was demonstra
ted by simultaneous immunohistochemical labeling of vascular elements and m
edullary TE. Medullary TE was often arranged as perivascular cuffs surround
ing intermediate-sized vessels, but was not associated with either the capi
llary network or large centrally located vessels. Similar analyses of RAG-2
(-/-) thymi revealed a striking physical association of medullary TE with v
ascular elements. Ultrastructural analysis of the RAG-2(-/-) thymus indicat
ed a preferential association of focal accumulations of medullary TE with p
ostcapillary venules. These data suggest that discrete segments of the thym
ic vasculature provide cues that act in concert with thymocyte-derived stim
uli to effect normal development of the thymic environment.