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Cytoskeletal‐based molecular motors produce force perpendicular to their direction of movement. However, it remains unknown whether and why motor proteins generate sidesteps movement along their filamentous tracks in vivo. Using Hessian structured illumination microscopy, we located green fluorescent protein (GFP)‐labeled intraflagellar transport (IFT) particles inside sensory cilia of live Caenorhabditis elegans with 3–6‐nanometer accuracy and 3.4‐ms resolution. We found that IFT particles took sidesteps along axoneme microtubules, demonstrating that IFT motors generate torque in a living animal. Kinesin‐II and OSM‐3‐kinesin collaboratively drive anterograde IFT. We showed that the deletion of kinesin‐II, a torque‐generating motor protein, reduced sidesteps, whereas the increase of neck flexibility of OSM‐3‐kinesin upregulated sidesteps. Either increase or decrease of sidesteps of IFT kinesins allowed ciliogenesis to the regular length, but changed IFT speeds, disrupted axonemal ninefold symmetry, and inhibited sensory cilia‐dependent animal behaviors. Thus, an optimum level of IFT kinesin sidestepping is associated with the structural and functional fidelity of cilia. Synopsis: Kinesin sidestepping has been observed in vitro, but its physiological relevance has not been investigated in vivo. In this study, optimal sidestepping of intraflagellar transport (IFT) kinesins in Caenorhabditis elegans sensory neurons is shown to regulate proper axoneme symmetry and animal chemosensation. IFT particles take sidesteps along axoneme microtubules, demonstrating torque generation of IFT motors in a living animal.Coordinated movement of kinesin‐II and OSM‐3 kinesin generates an intermediate level of sidestepping.Aberrant sidestepping allows ciliogenesis, but disrupts axonemal nine‐fold symmetryAberrant sidestepping inhibits sensory cilia‐dependent chemosensation. [ABSTRACT FROM AUTHOR]