Cilia are complex cellular protrusions consisting of hundreds of proteins. Defects in ciliary structure and function, many of which have not been characterised molecularly, cause ciliopathies, a heterogeneous group of human syndromes. Here we report on the FOXJ1 target gene Cfap206, orthologues of which so far have only been studied in Chlamydomonas and Tetrahymena. In mouse and Xenopus, Cfap206 was co-expressed with and dependent on Foxj1. CFAP206 protein localised to the basal body and to the axoneme of motile cilia. In Xenopus crispant larvae ciliary beat frequency of skin multiciliated cells was enhanced and bead transport across the epidermal mucociliary epithelium was reduced. Likewise, Cfap206 knockout mice revealed ciliary phenotypes. Electron tomography of immotile knockout mouse sperm flagella indicated a role in radial spokes formation reminiscent of FAP206 function in Tetrahymena. Male infertility, hydrocephalus and impaired mucociliary clearance of the airways in the absence of laterality defects in Cfap206 mutant mice suggests that Cfap206 may represent a candidate for the subgroup of human primary ciliary dyskinesia caused by radial spoke defects.