The thymus represents an epithelial microenvironment specialized in the generation of T-cells. The mechanisms or signals that determine the initial differentiation of the two well distinguished histological compartments of the thymus, cortex and medulla, remain unknown. Here, we report a three-dimensional analysis of the distribution of some established thymic epithelial markers in relation to thymic anatomical development during the first steps of thymus organogenesis. In the thymic primordium, initial lumen is lined by claudin (Cld)3/4+K5+ cells, after thymus growth and lobulation they form a continuous branched structure that increases its length and branching degree. Within it, the presence of luminal structures can be distinguished, even at E13.5. The medullary marker mouse thymic stroma 10 (MTS10) is upregulated in these Cld3/4+ lumen forming cells in a proximal-distal sequence. This structural organisation is histologically similar to that described in other epithelial organs undergoing a branching morphogenesis process. These results indicate that the thymic medulla can be evidenced as a continuous branched structure from early stages and suggest a thymic developmental program based on or containing elements of a branching morphogenesis program modified by the presence of lymphoid cells, in which medullary epithelial cell commitment is initially determined by lumen formation.