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High-speed machine technology with magnetically levitated rotor systems has become interesting solution in modern compressor, pump and turbo applications. Often, the commissioning of such machines is system identification-based with injected artificially generated excitation. In this paper a statistically uncorrelated PRBS design is proposed for multi-input multi-output MIMO system that gives the possibility to utilize same PRBS signal for all inputs. The proposed routine is validated with an experimental high-speed generator with active magnetic bearings (AMBs). The obtained frequency responses are validated by comparing the results with the mathematical model.