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Industrial Control Systems (ICS) are used for monitoring and controlling critical infrastructures such as power stations, waste water treatment facilities, traffic lights, and many more. Lately, these systems have become a popular target for cyber attacks. Both during their design and while operational, security is often an afterthought, leaving them vulnerable to all sorts of attacks. This paper presents a formal approach for analysing the security of Industrial Control Systems. A knowledge-based system, namely IDP, is used to analyse a model of the control system and extract system vulnerabilities. In this paper we present the input model of the methodology and the inferences and queries that allow the system to extract vulnerabilities. This methodology has been added to an existing framework where the user can model his system in the modeling language SysML. This SysML model then gets parsed into suitable IDP input. A fully working prototype has been developed and the approach has been validated on a real case study.