A method for monitoring a fly height of a magnetic transducer comprises flying the magnetic transducer at a distance of separation from a recording media. The fly height is modulated with a predetermined modulation frequency with a fly height control device. A read-back signal is read from the recording media with the magnetic transducer. A change of the read back signal is measured that results from modulating the fly height. A fault signal is provided in response to the change crossing a threshold.