A disk drive is disclosed comprising a head actuated over a disk comprising a plurality of data tracks. First data is written to a first data track, and the first data is read from the first data track to measure a first quality metric representing a recording quality of the first data. Second data is written to a second data track, and the second data is read from the second data track to measure a second quality metric representing a recording quality of the second data. The first and second quality metrics are processed to generate a first statistical quality metric. A first defect threshold is generated based on the first statistical quality metric, and at least part of the disk is scanned for defects based on the first defect threshold.