Haematopoietic clusters – cell aggregates that are associated with endothelium in the large blood vessels of midgestation vertebrate embryos – play a pivotal but poorly understood role in the formation of the adult blood system. To date, the opaqueness of whole embryos has prevented the systematic quantitation or mapping of all the haematopoietic clusters in mouse embryos but, on p. 3651, Tomomasa Yokomizo and Elaine Dzierzak remedy this situation. Using a technique to make whole mouse embryos transparent, combined with immunostaining and three-dimensional confocal microscopy, they show that the number of clusters peaks at embryonic day 10.5. Clusters are heterogeneous, they report, and localise to specific vascular subregions, such as the middle subregion of the aorta near to its junction with the vitelline artery. Finally, by combining flow cytometry and functional studies, the authors demonstrate that haematopoietic progenitor and stem cells are enriched within the cluster population. Together, these results provide novel insights into the spatial development of the adult blood system in mice.