A method for determining a flying height of a head of a hard disk drive. The disk drive includes a pre-amplifier and an automatic gain control ("AGC") circuit that are connected to the head. The method includes determining a first automatic gain control value based on AGC values at two delta pre-amplifier gain settings. A second automatic gain control value is determined based on AGC values at two different flying heights. A difference between the flying heights can be determined from the first and second automatic gain control values. If one of the flying heights is set to 0 the difference in gain values is equal to the flying height of the head.