A magnetic storage device includes a magnetic disk having a protective film and a lubricant layer formed on the protective film, a head stack assembly including a head operable to read information from and write information to the magnetic disk, and a suspension configured to support the head, a vibration detection sensor operable to output a detection signal to detect vibration of the head stack assembly, and an extraction unit operable to extract a specific frequency range from the detection signal outputted by the vibration detection sensor, the specific frequency range including a natural frequency of the head stack assembly but not including a natural frequency of an air film on the head.