The present invention realizes a medical device guidance system capable of improving propulsion control characteristic. The capsule guidance system 1 includes a rotating electromagnetic field generating device 4 for generating a rotating electromagnetic field for applying from the outside of a subject into the subject; a capsule 3 to be inserted into the body cavity of the subject; a magnet 16 provided in this capsule 3 and acting on the rotating electromagnetic field generated by the rotating electromagnetic field generating device 4; a spiral projection portion 12 provided on the outer peripheral surface of the capsule 3 and converting the rotational movement generated by the magnet 16 into a thrust; a controller 6 for controlling the rotating electromagnetic field generating device 4 to continuously change the state of the rotating electromagnetic field generated by rotating electromagnetic field generating device 4; and a capsule rotational direction pattern generator 41 for interchanging the rotational directions of the rotating electromagnetic field generated by the rotating electromagnetic field generating device 4 for each set rotational direction.