The abolishment of the internal border checks and the common procedures at the external bordersfosters the decision-making of the European Union to establish large-scale IT systems in the area of freedom,security and justice. The decrease of the security deficit by the control of immigration flow consists of threeendeavours: the common border control policy, the common visa policy and the common asylum policy. The aimof this paper is to analyse and evaluate the development of the operational management of large-scale IT systemsin the area of freedom, security and justice. The development process of these systems is not more than theirintegration into the so-called IT Agency. This new regulatory agency was established in January 2012. It hasmerged the operational management tasks of the further developed version of SIS (the SIS II), VIS and EURODACand it is flexible to add other existing and potential new systems. Hence, the added-value of the IT Agency is to beassessed, since new technologies shall be harnessed to meet the requirements of enhancing security and facilitatingtravel at the external borders.