The thymus is the primary organ responsible for generating T cells. Although thymus development has been studied in mice, little is known about how the human thymus develops. Here (p. 2015), Clare Blackburn and colleagues provide a comprehensive analysis of human thymus organogenesis. Using gene expression analyses, the researchers show that the spatial and temporal expression patterns of factors involved in thymus development in mice are conserved in humans. They also demonstrate that the human thymus arises from the third pharyngeal pouch, as in mice and in contrast to previous suggestions. Furthermore, they report, thymic epithelial cell differentiation as well as the immigration of mesenchymal cells and vascular progenitors into the human thymus occur after the onset of FOXN1 expression, consistent with the timing of these events in mice. Finally, the authors define precisely when the human thymus becomes colonised with haematopoietic cells, which are CD45+/CD7+/CD34int cells. Collectively, this study provides key insights into the conservation of thymus development between mice and humans, which has major clinical implications for enhancing or replacing thymus function.