Thymic epithelial cells, which create a three-dimensionally organized meshwork structure peculiar to the thymus, develop from simple epithelia of the third pharyngeal pouch and cleft during organogenesis. We comparatively investigated the thymus anlages of normal and nude mice by immunohistochemical analysis with regard to epithelial organization and distribution of hematopoietic progenitor cells at early stages of organogenesis. Our results show that development of the mouse thymus anlage at early stages can be subdivided into at least two stages by the differences in epithelial organization, i.e. stratified epithelial stage on embryonic day (Ed) 11 and clustered epithelial stage on Ed12. At the former stage, hematopoietic progenitor cells are accumulated in the mesenchymal layer of the thymus anlage, and at the latter stage progenitor cells enter the epithelial cluster and proliferate. In nude mice, hematopoietic progenitor cells are found in the mesenchymal layer on Ed11.5, but they are not observed among epithelial cells on Ed12, even though epithelial cells form a cluster structure. The present results suggest that aberrant development of the nude mouse thymus anlage occurs at the clustered epithelial stage and that epithelial cells of the nude anlage lack the ability to induce the entrance of hematopoietic progenitor cells into the epithelial cluster.