This book constitutes the refereed proceedings of the IEEE International Conference on Intelligence and Security Informatics, ISI 2006, held in San Diego, CA, USA, in May 2006. The 39 revised full papers, 30 revised short papers, and 56 extended poster abstracts presented were carefully reviewed and selected for inclusion in the book. The papers are organized in topical sections on intelligence analysis and knowledge discovery; access control, privacy, and cyber trust; surveillance and emergency response; infrastructure protection and cyber security; terrorism informatics and countermeasures; emerging applications; data analysis, knowledge discovery, and information dissemination; access control, privacy, and cyber trust; surveillance, bioterrorism, and emergency response; infrastructure protection and cyber security; data analysis and knowledge discovery; data, information, and knowledge management; threat detection, surveillance, and emergency response; as well as infrastructure protection and cyber security.