In the present study, we demonstrate that loss of the ciliary Frizzled-like receptor TMEM67, which is mutated in the ciliopathies MKS and JBTS, causes a severe cerebellar hypoplasia phenotype due to complex Wnt signalling, ciliogenesis and rostral hindbrain patterning defects that impact on downstream Shh signalling events. This evidence concerns the gene TMEM67 and Joubert syndrome.