Embodiments of the present invention provide a magnetic disk drive, in which a disturbance component contained in an output signal from a rotational vibration detector, can be appropriately suppressed irrespective of frequency of the component, and a method of controlling the drive. According to one embodiment, in a magnetic disk drive having a rotational vibration detector for detecting rotational vibration of a drive housing, a main control circuit performs a head moving step of driving a voice coil motor to move a magnetic head on a magnetic disk, a frequency estimation step of estimating a frequency of each disturbance component contained in an output signal from the rotational vibration detector after moving the magnetic head, and a suppressor setting step of setting a notch filter for suppressing the disturbance component based on the estimated frequency.