Cyber-physical systems (CPSs) are expected to collect, process, and exchange data that regularly contain sensitive information. CPSs may, for example, involve a person in the privacy of her home or convey business secrets in production plants. Hence, confidentiality, integrity, and authenticity are of utmost importance for secure and privacy-preserving CPSs. In this chapter, we present and discuss emerging security and privacy issues in CPSs and highlight challenges as well as opportunities for building and operating these systems in a secure and privacy-preserving manner. We focus on issues that are unique to CPSs, for example, resulting from the resource constraints of the involved devices and networks, the limited configurability of these devices, and the expected ubiquity of the data collection of CPSs. The covered issues impact the security and privacy of CPSs from local networks to Cloud-based environments.