Primary cilium is a membrane-protruding sensory organelle, which is organized from a basal body in G0/G1 phase cells. The resorption of primary cilia under specific growth factor stimuli is coupled to cell cycle re-entry and cell proliferation, and the proliferative function is vital for the organization of organs at an embryonic stage. In fact, abnormalities in ciliogenesis and/or cilium-derived signaling lead to malformation of various organs, such as the brain, eyes, nose, ear, heart, lung, liver, kidney, and bones. The inborn genetic disorders are collectively called 〝ciliopathy〟. However, the pathogenesis of the ciliopathies has largely remained unexplained, especially little is known about the cellular machinery that controls the ciliary resorption. Tctex-1 (t-complex testis expressed-1), one of the light chains of cytoplasmic dynein complex, regulates intracellular trafficking along microtubule. Tctex-1 phosphorylated at Thr94 is, in turn, free from the dynein complex to execute dynein-free functions. This review summarizes the current situation of the mechanisms of ciliary resorption with a central focus on the role of phosphorylated Tctex-1.