The Second International Workshop on Computational Intelligence for Security in Information Systems (CISIS’09) presented the most recent developments in the dynamically expanding realm of several fields such as Data Mining and Intelligence, Infrastructure Protection, Network Security, Biometry and Industrial Perspectives. The International Workshop on Computational Intelligence for Security in Information Systems (CISIS) proposes a forum to the different communities related to the field of intelligent systems for security. The global purpose of CISIS conferences has been to form a broad and interdisciplinary meeting ground offering the opportunity to interact with the leading industries actively involved in the critical area of security, and have a picture of the current solutions adopted in practical domains. This volume of Advances in Intelligent and Soft Computing contains accepted papers presented at CISIS’09, which was held in Burgos, Spain, on September 23rd-26th, 2009.