Complex urban structures are exposed to a variety of security risks. Especially concerning man-made hazards, cities can be considered as particularly vulnerable. Due to their high concentration of population, technical and social infrastructure, as well as their importance in politics, culture, economy and finance, metropolitan areas, in particular, can be considered as vulnerable environments. Since not every part of an urban area is exposed to the same level of potential security threats, it can be assumed that this level differs regionally within a metropolis. Based on methods of geoinformation science, this paper presents an innovative approach to identify particularly vulnerable urban regions. Using the 3D city model of the German capital Berlin as an example, the potential of such models for mapping, analysis and assessment of different threat levels in urban environments is demonstrated. This geovisual and analytical potential of 3D city models can be instrumental for decision makers working in security agencies for both threat assessment and intuitive cartographic communication of spatial phenomena related to urban security issues.