HyperDeduplicator is a fast biometric deduplication system capable of deduplicating millions of biometric templates within a very short period of time. This high-performance deduplication system can be used with any large-scale biometric system in the back-end to deduplicate and check data for inconsistencies. Unlike other systems, HyperDeduplicator does not rely on slow and computing resource intensive one-to-many (1: N) biometric matching operations to Deduplicate large databases of fingerprints.