A capsule medical device guiding system, comprising: a capsule medical device that includes a permanent magnet and is configured to be introduced into a liquid in a subject; a magnetic field generating unit configured to generate a magnetic field to be applied to the permanent magnet to guide the capsule medical device, and configured to change a direction of the generated magnetic field in a three-dimensional space; and a control unit configured to cause the magnetic field generating unit: (i) to generate a variable magnetic field including a rotating magnetic field where a direction of a magnetic field is rotated on a plane (Pv) parallel to a vertical axis (Az), and a magnetic field for generating a magnetic attracting force for moving the permanent magnet in a downward direction of the vertical axis (Az) in order for the capsule medical device to rotate about an axis perpendicular to a long axis of the capsule medical device and to move vertically downward, and (ii) to generate simultaneously a magnetic field such that the plane (Pv) is pivoted about the vertical axis (Az) at a predetermined period in order for the capsule medical device to be pivoted about the vertical axis (Az), characterized by: the pivot period of the plane (Pv) about the vertical axis (Az) is set to be longer than a rotation period on the plane (Pv) of the rotating magnetic field so that the pivot of the plane (Pv) about the vertical axis (Az) does not influence the rotation of the rotating magnetic field. a capsule medical device that includes a permanent magnet and is configured to be introduced into a liquid in a subject; a magnetic field generating unit configured to generate a magnetic field to be applied to the permanent magnet to guide the capsule medical device, and configured to change a direction of the generated magnetic field in a three-dimensional space; and a control unit configured to cause the magnetic field generating unit: (i) to generate a variable magnetic field including a rotating magnetic field where a direction of a magnetic field is rotated on a plane (Pv) parallel to a vertical axis (Az), and a magnetic field for generating a magnetic attracting force for moving the permanent magnet in a downward direction of the vertical axis (Az) in order for the capsule medical device to rotate about an axis perpendicular to a long axis of the capsule medical device and to move vertically downward, and (ii) to generate simultaneously a magnetic field such that the plane (Pv) is pivoted about the vertical axis (Az) at a predetermined period in order for the capsule medical device to be pivoted about the vertical axis (Az), characterized by: (i) to generate a variable magnetic field including a rotating magnetic field where a direction of a magnetic field is rotated on a plane (Pv) parallel to a vertical axis (Az), and a magnetic field for generating a magnetic attracting force for moving the permanent magnet in a downward direction of the vertical axis (Az) in order for the capsule medical device to rotate about an axis perpendicular to a long axis of the capsule medical device and to move vertically downward, and (ii) to generate simultaneously a magnetic field such that the plane (Pv) is pivoted about the vertical axis (Az) at a predetermined period in order for the capsule medical device to be pivoted about the vertical axis (Az), characterized by: the pivot period of the plane (Pv) about the vertical axis (Az) is set to be longer than a rotation period on the plane (Pv) of the rotating magnetic field so that the pivot of the plane (Pv) about the vertical axis (Az) does not influence the rotation of the rotating magnetic field.