Disclosed is a disk drive to characterize misaligned servo wedges. A disk of the disk drive includes a plurality of circumferential tracks, in which, each track includes a plurality of servo wedges spaced sequentially around the circumference of the track wherein the servo wedges may be misaligned relative to the head of the disk drive that moves about a pivot. A servo controller is used to characterize the misaligned servo wedges relative to the head during a seek operation by implementing the following operations: commanding the head to perform a seek operation from a starting track to an ending track; obtaining samples of wedge-to-wedge time (WTWT) values corresponding to time intervals between identified servo wedges for sampled tracks traversed during the seek operation; calculating WTWT variations for each sample; and calculating a calibrated misalignment value for each sample based upon WTWT variations.