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This book constitutes the refereed proceedings of the Second Symposium on Intelligence and Security Informatics, ISI 2004, held in Tucson, AZ, USA in June 2004. The 29 revised full papers and 12 revised short papers presented together with 6 extended abstracts of posters and 3 panel discussion summaries were carefully reviewed and selected for inclusion in the book. The papers are organized in topical sections on bioterrorism and disease informatics; data access, privacy, and trust management; data management and mining; deception detection; information assurance and infrastructure protection; monitoring and surveillance; security policies and evaluation; and social network analysis.