Touchdown is detected between an R/W head and disk by determining the variance in the frequency domain of a baseline position error signal (PES) and a PES measured after incrementally increasing the DFH control signal. To quantify the variance in the frequency domain, a discrete Fourier transform of the baseline PES and of each PES produced for a given DFH control signal is used. A band-limited PES variance is used to improve touchdown detection, but is not a requirement of this method.