Small changes in a broadcast version of a base media item can be identified by performing a multi-level comparison of digital fingerprints. A fingerprint of a base media item is compared to a fingerprint of a media broadcast to determine whether a media item embedded in a broadcast is likely, to a first level of certainty, to be the base media item. A second, more stringent, match between the fingerprint of the base media item and loosely matched items can be used to identify potentially-altered versions of the base media item. Potentially-altered versions can be compared against each other, and resulting matches are flagged as altered base media items, which can be fingerprinted and tested against broadcast fingerprints in the same manner as the base media item.