Various embodiments of the present invention provide systems and methods for determining fly height. For example, a system for fly height determination is disclosed that includes a head assembly disposed in relation to a storage medium, a write channel, and a read circuit. The read circuit is operable to receive information from both the head assembly and the write channel. A frequency determination circuit is included that is operable to receive a first signal from the read circuit corresponding to information received from the write channel and to provide a first fundamental frequency and a first higher order frequency based on the first signal, and the frequency determination circuit is operable to receive a second signal from the read circuit corresponding to information received from the head assembly channel and to provide a second fundamental frequency and a second higher order frequency based on the second signal. A compensation variable calculation module is included that is operable to divide the first fundamental frequency by the first higher order harmonic to yield a compensation variable. A fly height calculation module is included that is operable to divide the second fundamental frequency by the second higher order harmonic and the compensation variable to yield an indication of a distance between the head assembly and the storage medium.