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In conventional hard disk drives, a control system compensates for vibration in which the frequency is higher than the Nyquist frequency by using a multi-rate filter that decreases the gain above the Nyquist frequency. However, such a control system can only avoid instability and cannot suppress disturbances above the Nyquist frequency. To overcome this problem, a control system design method that suppresses disturbances beyond the Nyquist frequency is proposed. This method uses frequency responses of a controlled object and a digital controller to calculate the gain of the sensitivity function in a sampled-data system without requiring complex calculations involving matrices, and realizes a stable resonant filter that decreases the gain of the sensitivity function above the Nyquist frequency. Significant suppression of the vibrations caused by the disturbances beyond the Nyquist frequency is demonstrated by implementing this method in the head-positioning system of a hard disk drive.