Abstract: A patterned-media magnetic recording disk drive compensates for circumferential misalignment of data island patterns among the data tracks as a result of errors in fabrication of the master template used to make the disks. Each data track on the disk has its pattern shifted from a generally radial or arcuate line by a certain amount of pattern circumferential misalignment (PCM). The disk drive includes a write clock where writing to the data islands is controlled by detection of synchronization marks by the read head, and circuitry to adjust the phase of the write clock to compensate for PCM. The phase difference between the data pattern of the selected data track where data is to be written and the data pattern of the track where the synchronization marks are being detected is the difference in their respective PCM values.