In this chapter, we provide an overview of cyber-physical security applied to human machine systems (HMS), including a basic taxonomy, reference models, historical background and state-of-the-art. We discuss the most relevant technical contributions in the field of secure HMS by highlighting current trends, challenges, opportunities, and future directions. In particular, we will explore security paradigms integrating human-related factors, with a focus on data privacy, the Internet of Things, and computer security. Secure HMS are even more relevant in the context of future trustworthy autonomous systems, which will be required to detect and counteract evolving threats through intelligent behaviors based on learning and adaptation.