A method and apparatus is provided for measuring a media thermal decay rate for a disk in a disk drive. In one embodiment, reference patterns are written in a plurality of reference sectors on a test track of a disk surface. A thermal decay measurement duration is predetermined. After at least two decades of time longer than the predetermined thermal decay measurement duration have passed since writing the reference patterns in the plurality of reference sectors, sector-under-test patterns are written in a plurality of sectors-under-test, wherein the sectors-under-test and the reference sectors are written in data sectors and alternate with one another about at least a portion of the test track. The mean square error is measured and averaged for the reference sectors, and the mean square error is measured and averaged for the sectors under test. The averaged mean square error for the reference sectors and the averaged mean square error for the sectors-under-test are used to calculate the media thermal decay rate. In another embodiment, information associated with the amplitude of the readback signal is used instead of, or in addition to, the mean square error of the readback signal to calculate the media thermal decay rate.