Cell-cell communication via the Wnt signalling pathway is crucial for a plethora of developmental processes, including establishing the animal body plan, organogenesis and maintaining the stem cell niche. Although Wnt signalling is conserved in animals, it is also highly complex; the mammalian genome encodes 19 Wnt ligands, all of which are unique and essential, as well as 10 Frizzled receptors. Why, however, are there so many Wnt genes? Paula Murphy and colleagues address this question using sophisticated analyses to systematically map, in three dimensions, the in situ hybridisation expression patterns of Wnt pathway components in the mouse at embryonic day (E) 9.5, E10.5 and E11.5. Using this detailed atlas, combined with Wnt signalling reporter data, the authors can determine overlapping domains of different Wnt components and compare patterns of paralogous Wnt genes in relation to each other. For example, the researchers show that Wnt signalling is active in the ventral diencephalon, where Tcf/Lef transcription factors are expressed and Sfrp expression restricted; however, in a substantial part of the region, no Wnt or Fzd expression is detected. In addition, they identify ‘hot spots’ where several Wnt genes are co-expressed. Overall, these data provide a valuable resource for the study of Wnt signalling during embryogenesis.