The thymic stroma primarily comprises epithelial, mesenchymal and endothelial cells, interspersed with those of haematopoietic origin. Thymic epithelial cells (TECs) are highly heterogeneous, but can be divided into two broad lineages, cortical and medullary, based on phenotype, functionality and location. A population of Plet1+ TEC progenitors have been identified which, when isolated from mouse E12.5 or E15.5 fetal thymus, reaggregated, and grafted, can produce a functional thymus. However, the potential of individual progenitors to form cortex and/or medulla is undefined. The main aim of this thesis was to use retrospective clonal analysis to ascertain the point during thymus ontogeny at which the cortical and medullary lineages diverge. To this end, I used transgenic mice carrying a ubiquitous ROSA26laacZ reporter gene (where a duplication within lacZ encodes non-functional b-galactosidase). Here, rare, random laacZ-lacZ genetic recombinations result in heritable expression of functional b-gal, producing labelled clones. As this occurs at a known frequency, determination of TEC numbers would enable calculation of the expected number of TEC clones present throughout ontogeny. Due to the lack of quantitative data on all thymic cell populations, I determined the size not only of TEC (lin-EpCAM+), but also haematopoietic (CD45+), mesenchymal (lin-PDGFRa+ and/or lin-PDGFRb+) and endothelial (lin-CD31+) populations from E12.5 until E17.5. I then showed that the absolute number of Plet1+ TECs remains constant during this time, although the proportion of Plet1+ cells in cycle decreases. From these collective data, I propose a model for the role of the Plet1+ population in thymus development, in which Plet1+ cells continually give rise to Plet1- TECs in a self-renewing manner. Finally, I present a ‘dual origin coefficient’ strategy for analysis of a library of prospective TEC clones. I calculated the number of TEC lacZ+ clones expected to be present throughout thymus ontogeny, selecting an appropriate developmental stage for analysis. Although I observed several clones of apparent mesenchymal origin, supporting a single origin for intrathymic and capsular mesenchyme at E15.5, I observed no TEC clones in this extensive analysis. The CpG content of the ROSA26 promoter suggests a possibility of methylation-induced silencing brought about by de novo methylation of the lacZ reporter gene.