Modern storage systems are employing data deduplication with increasing frequency. Often the storage systems on which these techniques are deployed contain important data, and utilize fault-tolerant hardware and software to improve the reliability of the system and reduce data loss. We suggest that data deduplication introduces inter-file relationships that may have a negative impact on the fault tolerance of such systems by creating dependencies that can increase the severity of data loss events. We present a framework composed of data analysis methods and a model of data deduplication that is useful in studying the reliability impact of data deduplication. The framework is useful for determining a deduplication strategy that is estimated to satisfy a set of reliability constraints supplied by a user. © 2011 IEEE.