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In medical diagnoses and treatments, e.g., endoscopy, dosage transition monitoring, it is often desirable to wirelessly track an object that moves through the human GI tract. In this paper, we propose a magnetic localization and orientation system for such applications. This system uses a small magnet enclosed in the object to serve as excitation source, so it does not require the connection wire and power supply for the excitation signal. When the magnet moves, it establishes a static magnetic field around, whose intensity is related to the magnet's position and orientation. With the magnetic sensors, the magnetic intensities in some predetermined spatial positions can be detected, and the magnet's position and orientation parameters can be computed based on an appropriate algorithm. Here, we propose a real-time tracking system developed by a cubic magnetic sensor array made of Honeywell 3-axis magnetic sensors, HMC1043. Using some efficient software modules and calibration methods, the system can achieve satisfactory tracking accuracy if the cubic sensor array has enough number of 3-axis magnetic sensors. The experimental results show that the average localization error is 1.8 mm.