The emergence of interconnected cyber-physical systems and sensor/actuator networks has given rise to advanced automation applications, where a large amount of sensor data is collected and processed in order to make suitable real-time decisions and to achieve the desired control objectives. However, in situations where some components behave abnormally or become faulty, this may lead to serious degradation in performance or even to catastrophic system failures, especially due to cascaded effects of the interconnected subsystems. The goal of this presentation is to motivate the need for health monitoring, fault diagnosis and security of interconnected cyber-physical systems and to provide a methodology for designing and analyzing fault-tolerant cyber-physical systems with complex nonlinear dynamics. Various detection, isolation and accommodation algorithms will be presented and illustrated, and directions for future research will be discussed.