This paper investigates the application of the Schengen Information System (SIS) in the European Union and the balance between civil liberties, security and justice. It provides an overview of the SIS, technical issues related to the maintenance of the SIS, and transnational legal issues in the context of national security and public policy. Given that citizens can now move freely between States in Europe, the paper investigates how the SIS is being administered, applied, and enforced and some of the potential problems that arise from cross mutual state recognition of SIS alerts. This paper argues that the SIS has a number of inherent and propagating weaknesses and that the risk exposure presented to citizens is far too great for the benefits that ensue. The paper recommends a movement away from the idea of a fortress Europe toward one of State to State harmonization in transnational criminal issues.