This paper describes the design of the Cipherbase system. Cipherbase is a full-fledged SQL database system that achieves high performance and high data confidentiality by storing and processing strongly encrypted data. The Cipherbase system incorporates customized trusted hardware, extending Microsoft’s SQL Server for efficient execution of queries using both secure hardware and commodity servers. This paper presents the design of the Cipherbase secure hardware and its implementation using FPGAs. Furthermore, this paper shows how we addressed hardware / software co-design in the Cipherbase system.