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In the present paper, a novel model-based identification algorithm is developed to estimate the unbalance and AMB misalignment in a rigid rotor system levitated with active magnetic bearings (AMBs). For this, a mathematical model for an unbalanced and misaligned rigid rotor system consisting of a rigid rotor levitated by two active magnetic bearings has been developed. Two cases of the misalignment depending upon the amount of radial offset between the rigid rotor and active magnetic bearings have been examined for the investigation. In the first case, an unknown misalignment is considered that is to be estimated. In the second case, a trial misalignment is added in addition to the unknown misalignment. This is a novel concept proposed in line with the trial unbalance in rotor dynamic balancing. The equations of motion of the rigid rotor-misaligned AMB system are derived and numerically simulated to generate the time-domain rotor displacement and controlling current responses, which are further converted into frequency-domain signals assisted by the fast Fourier transform analysis. These responses have been utilized in the identification algorithm to estimate the unbalance and force-displacement and force-current stiffnesses of misaligned AMBs as well as the misalignment amount between the rotor and AMBs. Estimations of unbalance and AMB misalignment parameters have also been carried out at multiple speeds as well as against various levels of measurement signal noise and modelling errors. The developed identification algorithm is found to be effective and robust against these noise and modelling errors.