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Motile cilia are cellular beating machines that play a critical role in mucociliary clearance, cerebrospinal fluid movement, and fertility. In the airways, hundreds of motile cilia present on the surface of a multiciliated epithelia cell beat coordinately to protect the epithelium from bacteria, viruses, and harmful particulates. During multiciliated cell differentiation, motile cilia are templated from basal bodies, each extending a basal foot—an appendage linking motile cilia together to ensure coordinated beating. Here, we demonstrate that among the many motile cilia of a multiciliated cell, a hybrid cilium with structural features of both primary and motile cilia is harbored. The hybrid cilium is conserved in mammalian multiciliated cells, originates from parental centrioles, and its cellular position is biased and dependent on ciliary beating. Furthermore, we show that the hybrid cilium emerges independently of other motile cilia and functions in regulating basal body alignment. • Multiciliated cells contain a hybrid cilium with features of primary and motile cilium • The hybrid cilium originates from parental centriole • The hybrid cilium position is biased toward the cilia beating direction • The hybrid cilium functions in basal body alignment Liu, Nguyen et al. show that among hundreds of cilia of a multiciliated cell, there is one that differs from the others in structure, origin, and cellular position, and it participates in basal body alignment. [ABSTRACT FROM AUTHOR]