Abstract: A system and method for partitioning a data stream into a plurality of segments of varying sizes. A data stream manager partitions a received data stream into segments which are then conveyed to a deduplication engine for processing. The data stream received by the data stream manager includes metadata corresponding to the data stream. Based upon the metadata, which may include an indication as to a type of data included in the data stream, the data stream is partitioned into segments for further processing. A size of a segment used for partitioning given data is based at least in part on a type of data being partitioned. The variable segment sizes may be chosen to balance between maximizing the deduplication ratio and minimizing both the segment count and the size of the fingerprint index.