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Although RFID has become a widespread technology, the developers of numerous commercial systems have not taken care of security properly. This chapter presents a methodology for detecting common security flaws. The methodology is put in practice using an open-source RFID platform (Proxmark 3), and it is tested in different fields, such as public transportation or animal identification. The results obtained show that the consistent application of the methodology allows researchers to perform security audits easily and detect, mitigate, or avoid risks and possible attacks.