Cyber-Physical Systems, or Smart-Embedded Systems, are co-engineered for the integration of physical, computational and networking resources. These resources are used to develop an efficient base for enhancing the quality of services in all areas of life and achieving a classier lifestyle in terms of a required service’s functionality and timing. Cyber-Physical Systems (CPSs) complement the need to have smart products (e.g., homes, hospitals, airports, cities). In other words, regulate the three kinds of resources available: physical, computational, and networking. This regulation supports communication and interaction between the human word and digital word to find the required intelligence in all scopes of life, including Telecommunication, Power Generation and Distribution, and Manufacturing. Data Security is among the most important issues to be considered in recent technologies. Because Cyber-Physical Systems consist of interacting complex components and middle-ware, they face real challenges in being secure against cyber-attacks while functioning efficiently and without affecting or degrading their performance. This study gives a detailed description of CPSs, their challenges (including cyber-security attacks), characteristics, and related technologies. We also focus on the tradeoff between security and performance in CPS, and we present the most common Side Channel Attacks on the implementations of cryptographic algorithms (symmetric: AES and asymmetric: RSA) with the countermeasures against these attacks.