Provided are a method of calculating repeatable runout (RRO) of a hard disk drive (HDD) in a frequency domain, a method of calculating a compensation value using the RRO calculating method, and recording media used therefore. The method of calculating RRO in a disk with a plurality of tracks includes: calculating first set of frequency coefficients for representing the RRO by analyzing a position error signal (PES), which is sampled in a target track, in a frequency domain while a head follows the target track; and calculating the RRO using the first set of frequency coefficients.