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In this study we address the cross-axis effect (or error) problem in three-axis Anisotropic Magneto Resistance (AMR) magnetic sensors. We focus on magnetometer calibration in the Earth's magnetic field for low-cost sensors. We propose a self-consistent and practical method based on the cross-axis effect modeling, to compensate for the cross-axis effect without using any high precision magnetic sensors for comparing the results. This method does not depend also to other instruments to provide and measure the magnetic field. The compensation method is implemented in two configurations: direct amplification of an AMR signal and magnetization flipping. We show that the residual error with the compensation method in a non-flipped sensor is similar to that sensor in a using flipping.