It has been proposed that ciliated cells that produce a leftward fluid flow mediate left-right patterning in many vertebrate embryos. The cilia on these cells combine features of primary sensory and motile cilia, but how this cilia subtype is specified is unknown. We address this issue by analyzing the Xenopus and zebrafish homologs of Foxj1, a forkhead transcription factor necessary for ciliogenesis in multiciliated cells of the mouse. We show that the cilia that underlie left-right patterning on the Xenopus gastrocoel roof plate (GRP) and zebrafish Kupffer's vesicle are severely shortened or fail to form in Foxj1 morphants. We also show that misexpressing Foxj1 is sufficient to induce ectopic GRP-like cilia formation in frog embryos. Microarray analysis indicates that Xenopus Foxj1 induces the formation of cilia by upregulating the expression of motile cilia genes. These results indicate that Foxj1 is a critical determinant in the specification of cilia used in left-right patterning.