An in-vivo observation system provided with a capsule endoscope including an in-vivo observation section, a battery, a magnetic field detection section, a power supply switch that controls a power supply and a power supply control section that causes the power supply switch to operate according to an internal signal from the magnetic field detection section, and a magnetic field generating apparatus including a magnetic field generating section, an operation section that outputs an operation signal according to an operation by a user and a masking section that masks an operation signal inputted to the magnetic field generating section for a predetermined period.