A system and method for detecting duplicate checks during processing. The duplicate detection may be performed by a financial institution, such as a bank. The method may be implemented on a computer based system. The duplicate detection method may be automated. The method may be applied to incoming check files prior to processing of the check data to prevent processing of duplicate checks. The system and method may use a function, such as a hash function, to perform the duplicate detection. Other functions, such as a Bloom filter which may use multiple hash functions, may be used to perform the duplicate detection.