A capsule medical device guidance system (1; 201; 301) comprising: a capsule medical device that includes a magnetic field response unit; a magnetic field generating unit adapted to generate a magnetic field to the magnetic field response unit to guide the capsule medical device; an operation input unit (60; 260) adapted to input operation information to magnetically guide the capsule medical device; a control unit adapted to control the magnetic field generating unit to guide the capsule medical device according to the operation information input from the operation input unit (60; 260); and a selection unit adapted to select one of a contact mode and an away mode, the capsule medical device being brought into contact with a desired boundary surface in a plurality of boundary surfaces of a liquid in a subject in the contact mode, the capsule medical device being moved away from the desired boundary surface in the away mode, wherein the control unit controls the magnetic field generating unit to continuously generate the magnetic field such that a total force in the liquid of a buoyant force of the capsule medical device, a gravity of the capsule medical device, and a magnetic attraction force is oriented toward the desired boundary surface side when the selection unit selects the contact mode, and the control unit controls the magnetic field generating unit such that the total force in the liquid of the buoyant force of the capsule medical device, the gravity of the capsule medical device, and the magnetic attraction force is oriented toward a direction other than the direction oriented toward the desired boundary surface side when the selection unit selects the away mode, wherein the magnetic gradients of the magnetic fields which are generated when the contact and the away modes are selected are each a vertical magnetic gradient, characterized in that the operation input unit (60; 260) includes a magnetic field direction switching instruction unit (46; 346) that issues an instruction to select either the boundary surface on a vertically upper side or the boundary surface on a vertically lower side as the boundary surface of the liquid which the capsule medical device is brought into contact with or moved away from, and wherein control unit is adapted to change the direction of the magnetic gradient of the magnetic field which is generated by the magnetic field generating unit in each of the contact mode and the away mode according to the boundary surface that is selected by the magnetic field direction switching instruction unit (46; 346). a capsule medical device that includes a magnetic field response unit; a magnetic field generating unit adapted to generate a magnetic field to the magnetic field response unit to guide the capsule medical device; an operation input unit (60; 260) adapted to input operation information to magnetically guide the capsule medical device; a control unit adapted to control the magnetic field generating unit to guide the capsule medical device according to the operation information input from the operation input unit (60; 260); and a selection unit adapted to select one of a contact mode and an away mode, the capsule medical device being brought into contact with a desired boundary surface in a plurality of boundary surfaces of a liquid in a subject in the contact mode, the capsule medical device being moved away from the desired boundary surface in the away mode, wherein the control unit controls the magnetic field generating unit to continuously generate the magnetic field such that a total force in the liquid of a buoyant force of the capsule medical device, a gravity of the capsule medical device, and a magnetic attraction force is oriented toward the desired boundary surface side when the selection unit selects the contact mode, and the control unit controls the magnetic field generating unit such that the total force in the liquid of the buoyant force of the capsule medical device, the gravity of the capsule medical device, and the magnetic attraction force is oriented toward a direction other than the direction oriented toward the desired boundary surface side when the selection unit selects the away mode, wherein the magnetic gradients of the magnetic fields which are generated when the contact and the away modes are selected are each a vertical magnetic gradient, characterized in that the operation input unit (60; 260) includes a magnetic field direction switching instruction unit (46; 346) that issues an instruction to select either the boundary surface on a vertically upper side or the boundary surface on a vertically lower side as the boundary surface of the liquid which the capsule medical device is brought into contact with or moved away from, and wherein control unit is adapted to change the direction of the magnetic gradient of the magnetic field which is generated by the magnetic field generating unit in each of the contact mode and the away mode according to the boundary surface that is selected by the magnetic field direction switching instruction unit (46; 346).