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When developing cyber-physical systems such as automated vehicles, safety and cybersecurity analyses are often conducted separately. However, unlike in the IT world, safety hazards and cybersecurity threats converge in cyber-physical systems; a malicious party can exploit cyber-threats to create extremely hazardous situations, whether in autonomous vehicles or nuclear plants. We propose a framework for integrated system-level analyses for functional safety and cyber security. We present a generic model named Threat Identification and Refinement for Cyber-Physical Systems (TIRCPS) extending Microsoft’s six classes of threat modelling including Spoofing, Tampering, Repudiation, Information Disclosure, Denial-of-Service and Elevation Privilege (STRIDE). TIRCPS introduces three benefits for developing complex systems: first, it allows the refinement of abstract threats into specific ones as physical design information becomes available; Second, the approach provides support for constructing attack trees with traceability from high-level goals and hazardous events to threats. Third, TIRCPS formalizes the definition of threats such that intelligent tools can be built to automatically detect most of a system’s vulnerable components requiring protection. We present a case study on an automated-driving system to illustrate the proposed approach. The analysis results of a hierarchical attack tree with cyber threats traceable to highlevel hazardous events are used to design mitigation solutions.