This manipulator system has a medical instrument having a joint portion, a driving force transmission unit, a drive unit, and a driving force relay unit that can be switched between a driving force relay state and a driving force release state, and this manipulator system initialization method is provided with: a reference angle maintaining step in which the rotation angle of the joint portion is set to a reference angle, and the reference angle is maintained with the driving force relay unit switched to a driving force release state a drive unit connection step in which the driving force relay unit is switched to a driving force relay state with the joint portion disposed inside a body, which is the location where an initialization operation is performed and an origin setting step in which the joint portion is rotated from the reference angle by an angle that has been decided in advance, and then mapping of the drive origin of the drive unit is carried out in accordance with this rotation angle state.
