For various IT systems security is considered a key quality factor. In particular, it might be crucial for video surveillance systems, as their goal is to provide continuous protection of critical infrastructure and other facilities. Risk assessment is an important activity in security management; it aims at identifying assets, threats and vulnerabilities, analysis of implemented countermeasures and their effectiveness in mitigating risks. This paper discusses an application of a new risk assessment method, in which risk calculation is based on Fuzzy Cognitive Maps (FCMs) to a complex automated video surveillance system. FCMs are used to capture dependencies between assets and FCM based reasoning is applied to aggregate risks assigned to lower-level assets (e.g. cameras, hardware, software modules, communications, people) to such high level assets as services, maintained data and processes. Lessons learned indicate, that the proposed method is an efficient and lowcost approach, giving instantaneous feedback and enabling reasoning on effectiveness of security system.