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Most renal tubular epithelial cells possess primary cilia that protrude into the tubular lumen, where they are exposed to urine flow. The cilia of the epithelia curve with the urine flow within the renal tubules. The primary cilium of renal epithelium has been assumed to be a mechano-sensor of the urine flow. However, the mechanical characteristics of the cilium of an each cell are not well assessed. In this study, we measured Young's modulus of each primary cilium by using optical tweezers. First, we developed a system to manipulate each primary cilium of living tubular epithelial cells in situ by using optical tweezers. We adopted flexible-substratum technique to visualize individual micron-sized primary cilia of the Madin-Darby canine kidney (MDCK) cell lines. Through the use of the flexible-substratum technique, the primary cilia of MDCK cells could be clearly imaged from the side. We showed that we could apply minute force to polystyrene microspheres stuck on the tip of the cilia by using optical tweezers. The Young's modulus of each primary cilium was successfully examined by measuring the displacement of the microsphere. We concluded that this methodology enables us to manipulate each primary cilium minutely and to estimate the elasticity of an individual primary cilium.