Cells lining the lumen of various organs, such as the lung airway and the female reproductive tract, are multiciliated, and all the cilia are oriented in the same direction to generate flow. But how is cilia orientation coordinated within cells and across tissues? Chris Kintner and colleagues use the epithelial cells of Xenopus embryos as a model to study multicilate cell differentiation. On p. 3468, they identify a new regulator of cilia polarisation, the coiled-coil protein bbof1. Bbof1 is expressed in multicilate cells and localises to the axoneme and the basal body - the structure that determines cilia orientation. Upon bbof1 depletion, motile cilia still form, but are unable to generate significant flow because their orientation is disturbed. Notably, bbof1 is not required for the initial phase of cilia polarisation, but rather for the later refinement step, and for stabilising the alignment. Although the mechanism by which bbof1 acts remains unclear, this work identifies a key factor regulating cilia orientation and function.