Within the broad and growing spectrum of human ciliopathies is a range of linked and overlapping disorders that present with skeletal features. These have been coined the skeletal ciliopathies. The syndromes have, to this point, been largely attributed to alterations in cellular Hedgehog signalling during development. However, a huge surge in fundamental discovery and clinical research has unveiled a plethora of roles for cilia in biology. This implicates a range of molecular and cell processes in the pathogenesis of skeletal ciliopathies. Our understanding of bi-directional interactions between cilia and the extracellular matrix remains in its infancy. The identification of genes and causal mutations defines skeletal ciliopathies. Some of these genes, and the proteins they encode, are now being explored further, by means of cell, animal, and other model approaches, seeking to understand the molecular underpinnings of disease. However, given the relatively recent appreciation of links between cilia biology and human disease, there is much work to be done. This chapter will briefly introduce the primary cilium and its associated ‘ciliome’, before describing the ciliary-associated skeletal disorders and the genes with which they are associated. Where possible, it will expand upon our current mechanistic understanding.