Cilia are present on most cells of the body and their formation depends on intraflagellar transport (IFT). Mutations that affect IFT lead to altered sonic hedgehog (Shh) signalling, and consequently to limb and neural tube patterning defects in mice. Now, on p. 307, Bradley Yoder and co-workers reveal for the first time that IFT and therefore cilia are also required for normal Indian hedgehog (Ihh) signalling. They made their discovery using a conditional allele of an IFT protein, IFT88/polaris, to disrupt cilia and to investigate the effects on mouse limb development. Although cilia disruption in the ectoderm produces no phenotype, disruption in the mesenchyme results in polydactyly, a loss of anteroposterior digit patterning and a shortening of the proximodistal axis of the limb. Their results show that the digit-patterning phenotypes are associated with disrupted Shh activity. The limb outgrowth defects, however, are due to abrogated Ihh signalling during endochondral bone formation, the first evidence that IFT and normal cilia functioning are required for Ihh signalling.