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This paper analyzes two types of effects caused by the fundamental current in saliency-tracking-based techniques for sensorless control of three-pole active magnetic bearings, i.e., saturation and insufficient spectral separation of the fundamental current command during transients. Injection of a high-frequency signal superimposed to the fundamental excitation providing active control allows the measurement of changes in the air gap, from which an estimation of the rotor position can be obtained. Interference of the fundamental current, which is needed to operate the magnetic bearing, with the high-frequency current can occur through two mechanisms: 1) saturation; and 2) high-frequency harmonics caused by fast transients of the fundamental current. Both phenomena can interfere with the sensorless control resulting in a decrease in its performance. The effects caused by the fundamental current on the negative-sequence high-frequency current, used as a position estimation signal, are studied, and a decoupling mechanism is proposed. An analysis of high-frequency leakage flux is presented. and a simple analytical model is developed for describing the aforementioned phenomena. Finite-element analysis of the magnetic bearing under fundamental excitation, as well as experimental verification, is used to validate the analytical findings.