A system, method, and medium for dynamically scaling the size of a fingerprint index in a deduplication storage system. Fingerprints are stored as entries in a fingerprint index, and the fingerprint index is scaled to fit into an in-memory cache to enable fast accesses to the index. A persistent copy of the full fingerprint index is stored on a non-volatile memory. The cached fingerprint index uses binary sampling to categorize half of the fingerprint entries as samples and protected, and the other half of the entries as non-samples and replaceable. When a search of the cached index results in a hit on a sample entry, all of the non-sample entries associated with the same container are copied from the persistent index to the cached index.