The present invention provides for a system and method for assuring integrity of deduplicated data objects stored within a storage system. A data object is copied to secondary storage media, and a digital signature such as a checksum is generated of the data object. Then, deduplication is performed upon the data object and the data object is split into chunks. The chunks are combined when the data object is subsequently accessed, and a signature is generated for the reassembled data object. The reassembled data object is provided if the newly generated signature is identical to the originally generated signature, and otherwise a backup copy of the data object is provided from secondary storage media.