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This paper investigates the influence of stator current and machine saliency on rotor position estimation of permanent magnet synchronous machine (PMSM) based on third harmonic back-EMF which is contained in windings irrespective of the operational mode and parameters. Due to machine saliency and saturation of air gap flux-linkage, the amplitude and phase angle of third harmonic back-EMF will be affected by the stator current. Several experimental analyses are carried out based on a dSPACE platform with a laboratory PMSM validate that the machine speed and q-axis current will not affect the phase angle of the third harmonic back-EMF, whereas there will exhibit rotor position estimation error by applying negative d-axis current, and with large positive d-axis current, the third harmonic back-EMF will be seriously distorted due to critical air gap saturation.