Understanding how genetic factors contribute to obesity is key to identifying potential therapeutic avenues of study, but to date the major genetic risk factors that predict an obese phenotype remain elusive. The study of simpler genetic causes of obesity, such as isolated phenotypes or in syndromic form, although of limited relevance to the genetic load of common disease, has nonetheless shown promise in identifying important adipogenic pathways. In this chapter, we discuss the links between obesity and a discrete syndromic set of disorders, the ciliopathies. Cilia are conserved sensory organelles that protrude from the apical membrane of cells and play vital developmental and physiological roles in all vertebrates. Within the disease module of the ciliopathies, Bardet–Biedl and Alström syndromes share obesity due to hyperphagia as a defining trait. Moreover, mouse genetic models and in vitro experiments suggest a positive role for cilia in leptin signaling in the hypothalamus and a negative role for cilia in the formation of adipocytes in peripheral tissues, offering two potential explanations on how ciliary lesions lead to obesity. We focus on recent advances in vivo and in vitro that further our understanding of how malfunctioning cilia contribute to the dysregulation of energy homeostasis on a molecular mechanistic level.