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This paper provides a taxonomy of secure software systems engineering (SSE) by surveying and organizing relevant SSE research and presents current trends in SSE, on-going challenges, and models for reasoning about threats and vulnerabilities. Several challenging questions related to risk assessment/mitigation (e.g., “what is the likelihood of attack”) as well as practical questions (e.g., “where do vulnerabilities originate” and “how can vulnerabilities be prevented”) are addressed.