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Significant efforts are underway to modernise global air traffic management systems. This will result in a level of connectivity between different systems that has never before been achieved, creating a `system of systems' that requires a very high level of dependability. To achieve this dependability, security must be designed-in rather than relying on hardening of systems post implementation. This is also expected to minimise the costs of security. The European ATM modernisation programme, SESAR, has been taking a systems engineering approach to ensure that R&D is rapidly transferred to industrialisation and then deployment. This approach has been applied to security, organised around `operational focus areas' that represent discrete operational improvements. In such a complex programme, traditional risk analysis and mitigation was thought to be limited when attempting a system wide coherence for security. Hence the SESAR programme is adopting a `security case' approach, drawing on lessons learned in safety cases, validation & verification of ATM R&D, and aligned to the system engineering approach.