A capsule guidance system (10; 30; 40; 50), comprising: a capsule medical device adapted to be inserted into an organ of a subject and comprising: a magnet disposed in the center of the capsule medical device; transmitting electrodes (21 a, 21 b) formed respectively on the surfaces of opposing domes of a dome-shaped housing of the capsule medical device to form an electric potential distribution on the body surface of the subject; the capsule guidance system further comprising: a plurality of electrode pads adapted to be disposed on a body surface of the subject and adapted to detect electrical signals transmitted by the transmitting electrodes (21a, 21b) from the capsule medical device via the subject used as a communication medium; a magnetic guidance unit (15, 16, 18) adapted to apply a magnetic field to the capsule medical device to guide the capsule medical device; and a position calculation unit adapted to calculate the position of the capsule medical device based on the electrical signals from the capsule medical device, the capsule guidance system characterized by an eliminating unit that is adapted to eliminate signal components of eddy current from the electrical signals detected by the plurality of electrode pads, wherein the eddy current is generated in the subject due to a change in the magnetic field, and the electrical signals used by the position calculation unit for calculating the position of the capsule medical device are the electrical signals from which the signal components of the eddy current are eliminated by the eliminating unit. a capsule medical device adapted to be inserted into an organ of a subject and comprising: a magnet disposed in the center of the capsule medical device; transmitting electrodes (21 a, 21 b) formed respectively on the surfaces of opposing domes of a dome-shaped housing of the capsule medical device to form an electric potential distribution on the body surface of the subject; the capsule guidance system further comprising: a plurality of electrode pads adapted to be disposed on a body surface of the subject and adapted to detect electrical signals transmitted by the transmitting electrodes (21a, 21b) from the capsule medical device via the subject used as a communication medium; a magnetic guidance unit (15, 16, 18) adapted to apply a magnetic field to the capsule medical device to guide the capsule medical device; and a position calculation unit adapted to calculate the position of the capsule medical device based on the electrical signals from the capsule medical device, the capsule guidance system characterized by an eliminating unit that is adapted to eliminate signal components of eddy current from the electrical signals detected by the plurality of electrode pads, wherein the eddy current is generated in the subject due to a change in the magnetic field, and the electrical signals used by the position calculation unit for calculating the position of the capsule medical device are the electrical signals from which the signal components of the eddy current are eliminated by the eliminating unit. a magnet disposed in the center of the capsule medical device; transmitting electrodes (21 a, 21 b) formed respectively on the surfaces of opposing domes of a dome-shaped housing of the capsule medical device to form an electric potential distribution on the body surface of the subject; the capsule guidance system further comprising: a plurality of electrode pads adapted to be disposed on a body surface of the subject and adapted to detect electrical signals transmitted by the transmitting electrodes (21a, 21b) from the capsule medical device via the subject used as a communication medium; a magnetic guidance unit (15, 16, 18) adapted to apply a magnetic field to the capsule medical device to guide the capsule medical device; and a position calculation unit adapted to calculate the position of the capsule medical device based on the electrical signals from the capsule medical device, the capsule guidance system characterized by a plurality of electrode pads adapted to be disposed on a body surface of the subject and adapted to detect electrical signals transmitted by the transmitting electrodes (21a, 21b) from the capsule medical device via the subject used as a communication medium; a magnetic guidance unit (15, 16, 18) adapted to apply a magnetic field to the capsule medical device to guide the capsule medical device; and a position calculation unit adapted to calculate the position of the capsule medical device based on the electrical signals from the capsule medical device, the capsule guidance system characterized by an eliminating unit that is adapted to eliminate signal components of eddy current from the electrical signals detected by the plurality of electrode pads, wherein the eddy current is generated in the subject due to a change in the magnetic field, and the electrical signals used by the position calculation unit for calculating the position of the capsule medical device are the electrical signals from which the signal components of the eddy current are eliminated by the eliminating unit.