An in-vivo observation system includes a capsule endoscope and a magnetic field generating apparatus. The capsule endoscope includes an in-vivo observation section, a radio sending section, a battery, a magnetic field detection section for detecting a magnetic field signal, and a power supply control section for controlling state of power supply from the battery to the in-vivo observation section and the radio sending section by toggle operation based on a detection result by the magnetic field detection section. The magnetic field generating apparatus includes a magnetic field generating section, an operation switch for giving a command to start generating the magnetic field signal, a state determination section for determining the state of power supply, and a magnetic field generation control section for controling generation of the magnetic field signal based on the command from the operation switch and a determination result by the state determination section.