It is well known that cilia are important for hedgehog (Hh) signalling in mice, but their role in zebrafish has been somewhat contentious. On p. 3089, Huang and Schier now unambiguously demonstrate that zebrafish that lack cilia have normal Wnt, but disrupted Hh, signalling. The authors overcame the experimental problems posed by the maternal contribution of ciliary components by generating maternal-zygotic (MZ) mutants for oval, which encodes an intraflagellar transport protein that is essential for cilia formation. MZ oval mutants lack all cilia and have normal Wnt signalling; Hh signalling, however, is spatially expanded, but its levels are reduced. By comparison, mice with defective cilia have reduced Hh signalling levels due to the loss of gli1, a Hh signalling component that is entirely dependent on Hh signalling for its expression in mice, but not in zebrafish. Together, these findings reveal a conserved requirement for cilia in vertebrate Hh signalling, with distinct effects in mice and zebrafish owing to divergent gli1 regulation.