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In conventional hard disk drives, a control system compensates for the mechanical resonance above the Nyquist frequency by using sampled-data control theories or multirate control techniques. However, such a control system can only avoid instability and cannot suppress disturbances above the Nyquist frequency. In response to this problem, a control system design method that suppresses disturbances beyond the Nyquist frequency is proposed. This method uses the 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. When the method was applied to the head-positioning system of a hard disk drive, the experimental results showed that the control system suppressed disturbances that had the frequencies higher than the Nyquist frequency.