Intersampling vibrations of a sampled-data positioning control system may lead to degrade the performance and reliability of mechatronic products. Such vibrations are caused by mechanical resonances with frequencies beyond the Nyquist frequency of the control system. To address this problem, we analyzed residual vibrations using a shock response spectrum (SRS) analysis employed for characterizing transient characteristics of mechanical resonances. We showed that the acceleration input in sampleddata control systems excited the mechanical resonance near the sampling frequency during a period of settling to a target position. These phenomena were confirmed through experiments using the actual head-positioning system of the hard disk drive. Consequently the vibrations caused by the mechanical resonances around the sampling frequency were not only the difficult to observe but readily excited by the control input. Therefore, the sampled-data positioning control system must be designed such that the sampling frequency is away from mechanical resonances.