A capsule medical device guidance system includes a capsule medical device with a response unit a generating unit that generates a magnetic field to the response unit, an input unit that inputs operation information to magnetically guide the medical device, a control unit that controls the generating unit to guide the medical device according to the operation information, and a selection unit that selects a contact mode or away mode, for bringing the medical device into contact with a boundary surface in liquid in a subject in the contact mode, the medical device being moved away from the boundary surface in the away mode. The control unit generates the magnetic field in which a total force is oriented toward the boundary surface side, and the control unit controls the generating unit such that the total force is oriented toward a direction other than the direction for the away mode.
