In zebrafish embryos, motile cilia lining the Kupffer’s vesicle (KV; the fish equivalent of the mouse node) help to establish left-right (LR) asymmetry. Wnt/β-catenin signalling is also involved in this process but precisely how it functions is unclear. Xueying Lin and colleagues now reveal that Wnt/β-catenin signalling directly regulates ciliogenesis in the zebrafish KV (see p. 514). The researchers show that reduced Wnt signalling disrupts LR patterning and ciliogenesis and downregulates Foxj1, a transcription factor that is required for the biosynthesis of motile cilia. KV-specific expression of foxj1a, they report, requires the presence of putative Lef1/Tcf binding sites in the foxj1a enhancer region, which suggests that Wnt signalling activates fox1ja transcription directly. Importantly, reduction of Wnt signalling also impairs foxj1 expression and ciliogenesis in developing zebrafish pronephric ducts and otic vesicles, epithelial structures that require Wnt activity for their development and function. The researchers propose, therefore, that the regulation of Foxj1 expression and ciliogenesis by Wnt/β-catenin signalling is a general developmental mechanism in zebrafish.