Faced by serious challenges affecting competitiveness, sustainability and the safety and security of their inhabitants, cities' authorities are investing in complex infrastructure projects to make more intelligent and efficient use of resources. Investments include improved asset management through greater use of building information modelling (BIM) and introduction of complex cyber-physical systems in energy and transport sectors. Increased complexity of systems, particularly complex interactions between physical and cyber domains, create new cyber security challenges. An analysis methodology is described which enables multi-disciplinary teams to undertake a systematic analysis of building information and systems to identify safety, security or resilience issues. Examples of its application to building modelling and city infrastructure projects are discussed.