A guiding system includes a capsule medical device including a permanent magnet; a magnetic field generating unit to generate a magnetic field to the magnet to guide the capsule, and change a direction of the magnetic field in a three-dimensional space; and a control unit to control the magnetic field generated by the generating unit. Where the capsule is located on a liquid surface, the control unit generates a first magnetic field such that a plane, which is parallel to a vertical axis and in which a magnetic field including a rotating magnetic field where a magnetic field is rotated on the plane is generated, pivots about the vertical axis at a predetermined period and a second magnetic field for generating a magnetic attracting force for moving the magnet vertically downward to submerge the capsule in the liquid, the first and second magnetic fields being applied at a same time.