A capsule guiding system includes a magnetic guiding unit, a displaying unit, an operation unit, and a control unit. The magnetic guiding unit guides, using magnetic force, a capsule-shaped medical apparatus introduced inside a subject. The displaying unit displays an image of the subject and an image of the capsule-shaped medical apparatus as an overlapped image, and changes relative position and relative direction between the two images as the capsule-shaped medical apparatus is guided by the magnetic guiding unit. The operation unit inputs coordinate information which specifies movement direction of the capsule-shaped medical apparatus. The control unit adjusts coordinate system of the displaying unit and coordinate system of the operation unit to be consistent with each other, transforms the coordinate information input from the operation unit into the coordinate system of the magnetic guiding unit, and controls the guiding of the capsule-shaped medical apparatus based on the transformed coordinate information.
