In a magnetic recording disk drive, a disk with equally angularly spaced regions that have topography different from the other regions of the disk is used to detect head-disk contact. In one embodiment of a bit-patterned media (BPM) disk, equally angularly spaced servo sectors have topography different from the data regions of the disk. A head-disk spacing sensor detects the topography of the servo sectors as the servo sectors pass the sensor during rotation of the disk. This results in the head-disk spacing sensor generating an output signal with a fundamental frequency f0=NX/60 Hz, where N is the number of servo sectors and X is the disk rotation rate in RPM. A second or higher harmonic or harmonics of the fundamental frequency f0 are filtered from the output of the head-disk spacing sensor and used to identify the initiation of head-disk contact.