Ciliopathies are a group of human diseases that involve dysfunction of the cilium. Human patients with mutations in ciliary proteins can exhibit a wide range of phenotypes, one of which is obesity. This is seen in patients with Bardet-Biedl syndrome (BBS) and Alström syndrome (ALMS). Both of these disorders are caused by mutations in proteins that localize to the cilium or the basal body at the base of the cilium. These rare human disorders and their corresponding mouse models together with genetic approaches to disrupt cilia on specific cell types are beginning to uncover the connection between the cilium and energy homeostasis. Here we will review the current data on how cilia are thought to be involved in energy homeostatic pathways and discuss several key factors to consider when utilizing conditional approaches to evaluate ciliary function and their link to obesity.