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Perpendicular recording media noise is investigated with a microstructure model based upon magnetic clustering for irregular magnetization transitions. This model uses cylinders to account for the distribution of cluster diameters. Quantitative comparisons between experiments and calculations indicate that the cluster-size distribution of media can be estimated from the read/write properties. Estimates show that the cluster-size deviation of perpendicular recording media is somewhat larger than that of longitudinal recording media. Because calculations show that transition jitter depends strongly on the cluster-size distribution, reduction of the cluster-size deviation, as well as reducing the average cluster size, can significantly improve the signal-to-noise ratio of perpendicular recording media.