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There is a growing demand for large-scale distributed storage systems to support resource sharing and fault tolerance. Although heterogeneity issues of distributed systems have been widely investigated, little attention has yet been paid to security solutions designed for distributed storage systems with heterogeneous vulnerabilities. This fact motivates us to investigate a fragment allocation scheme called S-FAS to improve security of a distributed system where storage sites have a wide variety of vulnerabilities. In the S-FAS approach, we integrate file fragmentation with the secret sharing technique in a distributed storage system with heterogeneous vulnerabilities. Storage sites in a distributed systems are classified into a variety of different server types based on vulnerability characteristics. Given a file and a distributed system, S-FAS allocates fragments of the file to as many different types of nodes as possible in the system. Data confidentiality is preserved because fragments of a file are allocated to multiple storage nodes. We develop storage assurance and dynamic assurance models to evaluate the quality of security offered by S-FAS. Analysis results show that fragment allocations made by S-FAS lead to enhanced security because of the consideration of heterogeneous vulnerabilities in distributed storage systems.