To provide a position detection system, a guidance system, and a position detection method which allow a capsule medical device to be free from adjustment of an alternating magnetic field frequency for position detection and to be made more compact and less expensive.

The position detection system is characterized by having a frequency determining section 50B for obtaining a position calculating frequency used for calculating the position and the orientation of a capsule medical device 20 based on the resonance frequency of a magnetic induction coil of the capsule medical device 20, and a position analyzing means 50A for calculating the position and the orientation of the capsule medical device 20 based on the difference between outputs from magnetic sensors 52 when only an AC magnetic field is applied and those from the magnetic sensors 52 when the AC magnetic field and the induced magnetization are applied; and by limiting a frequency range of the AC magnetic field and/or an output frequency range of the magnetic field sensors used for analysis by the position analyzing means 50A based on the position calculating frequency.