The formation and elongation of polarised epithelial tubules is essential for the structure and function of several metazoan organ systems but the molecular mechanisms that regulate tubulogenesis are largely unknown. Here (p. 1774), Denise Marciano and colleagues provide new insights into tubulogenesis by studying the developing mouse nephron. The researchers show that kidney mesenchymal cells contain Par3-expressing microdomains on adjacent cells. These microdomains coalesce to form a continuous lumen, which elongates by extension and by additional de novo lumen formation. Both lumen formation and elongation require afadin, a nectin adaptor protein that is implicated in adherens and tight junction formation. Using mice that lack afadin in nephron precursors, the researchers demonstrate that afadin is required for the coalescence of Par3-expressing microdomains, which is needed to establish apical-basal polarity and generate a continuous lumen. These results reveal a novel mechanism for lumen formation and morphogenesis in vivo in which afadin plays a central role through its recruitment of polarity and junctional proteins to sites of lumen formation.