Evaluating all intrusion detection points in an end-to-end cyber-physical system can be challenging. This master thesis focuses on evaluating the security of the most exposed part of such systems, Radio Frequency Identification (RFID) communication. As both the RFID reader and tag can be located outside of secure premises, RFID communication can be a target of several cyber threats. Common cyber-attacks such as replay attacks, eavesdropping, or tag cloning can be associated with the lack of security of the communication channel between the reader and the tag or flaws of the implemented authentication protocols and encryption algorithms. This thesis briefly summarizes parts 4 and 3 of the ISO/IEC 14443 standard, which specify the initialization, selection, and transmission protocols in high-frequency RFID smart-card and reader communication. A formal security analysis was conducted to evaluate these protocols using a tool called Scyther. Then, an improved authentication protocol was proposed utilizing a commercially available feature, the Random Unique Identifier of the card (RID). The Scyther protocol verification results showed that implementing RID can prevent many RFID attacks such as, eavesdropping or replay attacks, and protect the cardholder's privacy.