Embodiments of the invention enable the flying of a slider to be lowered and increase recording density with a simple configuration in a magnetic disk apparatus. In one embodiment, a magnetic disk apparatus comprises a magnetic disk including tracks for recording data; a magnetic head slider disposed with a magnetic head that flies over the rotating magnetic disk and records data to, or plays back data from, the magnetic disk; and a control device that controls the operation of the apparatus. Slider flying height data that vary inside the tracks are prerecorded in the tracks of the magnetic disk. The control device controls the operation of the magnetic head slider with respect to the magnetic disk on the basis of the slider flying height data recorded in the tracks.