Purpose -In this paper, the aim is to present a modeling strategy for a flexible rotor/active magnetic bearing (AMB) system with non-collocation. Special attention is paid to the vibration reduction and the stable passage through the first critical speed. Design/methodology/approach -The finite element method based on Euller-Bernoulli beam theory is applied in the formulation of the rotor model. Since rotor/AMB systems are complex mechatronic systems, reduced order approach is used in the control system design. This study applies the modal decomposition method and the modal truncation method, thus retaining the lower order bending modes. The obtained numerical results are compared with the measured open loop frequency responses and the existing differences are compensated in order to obtain accurate numerical model. Findings -Frequency response of the entire system model (flexible shaft, actuators, power amplifiers and sensors) with amplitudes expressed in rotor lateral displacements can be verified by the measured frequency responses. The deviations in the amplitude and phase diagrams are then successfully corrected using the appropriate model modifications. Practical implications -The results of this research find direct applications in flexible rotors supported by AMBs, e.g. high speed spindles, turbo molecular pumps, flywheel energy storage systems, etc. The presented procedure can be especially valuable in the design of model based controllers. Originality/value -An AMB system model is developed and presented in this paper, in conjunction with a systematic description of an efficient procedure for the elimination of the typical mismatches between the simulation and experiment. Firstly, rotor/AMB test rig is stabilized with an appropriately tuned PID controller and an open loop frequency response is obtained for such a system. This response is then compared to corresponding simulation results for which mismatches are identified and eliminated thus yielding an accurate model of the system. COMPEL 32,4 1244 1. Introduction Active magnetic bearings (AMBs) present an alternative to conventional mechanical bearings in a variety of rotating machines, such as turbo molecular pumps, flywheels, machine tool spindles, etc. Their unique advantages, such as complete elimination of oil lubrication systems, absence of mechanical wear, low maintenance costs, programmable stiffness and damping, follow directly from their contactless suspension principle.Nevertheless, AMB systems are multivariable systems which require properly tuned feedback loops in order to ensure stable rotor suspension. Control of AMBs has been studied in many papers. The papers by Siegwart et al. (1991) and Lei and Palazzolo (2008) utilized linear PID controllers with associated filters, while papers Jastrzebski et al. (2010), Nonami and Ito (1996) and Schönhoff et al. (2000) deal with more advanced control strategies. If the rotor operates in the subcritical frequency range, a point mass or a rigid body model can be used to model the shaft. However, fo...