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Active magnetic bearings have been used in a rapidly growing number of applications such as jet engines, compressors, pumps and flywheel systems that are required to meet high speed, low vibration, zero frictional wear and clean environment specifications. The MBC 500 is a magnetic bearing system which includes an internal air turbine drive for a rotor that can reach a speed of ±10,000 RPM. In this paper, a project aiming to design and implement a speed controller for the air turbine is discussed. In order to design the speed controller, a model of the air turbine is identified using data collected in the frequency domain. Methods to overcome the difficulties encountered in system identification caused by the MATLAB μ-Analysis and Synthesis toolbox are addressed. The model obtained at a particular operating point using frequency response data is validated in the time domain. Since the system is nonlinear, a set of models has been obtained at different operating points and a nominal model is determined. The speed controller has been designed, on the basis of the nominal model, in both continuous and discrete time domains. The designed digital controller is implemented on a dSPACE DS1102 digital signal processor board and the controller designed in s-domain is implemented with an analogue circuit.