this book constitutes the refereed proceedings of the third international conference on advances in information security and its applications, isa 2009, held in seoul, korea, in june 2009. the 41 revised full papers presented were carefully reviewed and selected from 137 submissions. the papers are organized in topical sections on cryptographic algorithms, authentication and identity management, authorization and access control, biometrics and computer forensics, cryptographic protocols, data integrity and privacy, key management and recovery, mobile and rfid network security, firewall, ids, anti-virus, and other security products, internet and web services security, cyber-attack and cyber-terrorism, other security research, together with the articles from the workshops mowin 2009, nassue 2009, iawsn 2009, wngs 2009 & cgms 2009, shci-isa 2009.