The Second International Workshop on Computational Intelligence for Security in Information Systems (CISIS’09) presented the most recent developments in the - namically 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 Infor- tion 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 - rd th pers presented at CISIS’09, which was held in Burgos, Spain, on September 23 -26 , 2009. After a through peer-review process, the International Program Committee selected 25 papers which are published in this workshop proceedings. This allowed the Scientific Committee to verify the vital and crucial nature of the topics involved in the event, and resulted in an acceptance rate close to 50% of the originally submitted manuscripts.