A method is disclosed for performing a defect scan for a disk drive. Data is recorded on a first data area of a disk substantially free from defects and on a second data area of the disk substantially affected by at least one defect. A defect scan parameter is initialized with an initial setting. The first data area is read to determine a first defect threshold, and the second data area is read to determine a second defect threshold. A margin is saved representing a difference between the first and second defect thresholds. The setting for the defect scan parameter is adjusted, and the elements of reading the first and second data areas and saving a corresponding margin are repeated at least once. A setting is then selected for the defect scan parameter in response to the saved margins.