Provided are a method of protecting a head and a disk in a HDD from shocks and an apparatus therefor by detecting the movement of the HDD using the amount of jitter in servo signals and unloading the head when the movement is great enough to damage the head and the disk. The method of protecting the HDD from shocks includes: reading the servo signals from the rotating disk using the head that follows tracks on the disk, detecting an amount of jitter in the servo signals, comparing the detected amount of jitter with a predetermined threshold amount of jitter corresponding to a movement great enough to damage the head and the disk, and unloading the head if the detected amount of jitter is greater than the predetermined threshold amount of jitter.