Radio Frequency Identification (RFID) is a technology aimed at eficiently identifying and tracking goods and assets. Such identification may be performed without requiring line-of-sight alignment or physical contact between the RFID tag and the RFID reader, whilst tracking is naturally achieved due to the short interrogation field of RFID readers. That is why the reduction in price of the RFID tags has been accompanied with an increasing attention paid to this technology. However, since tags are resource-constrained devices sending identification data wirelessly, designing secure and private RFID identification protocols is a challenging task. This scenario is even more complex when scalability must be met by those protocols. Assuming the existence of a lightweight, secure, private and scalable RFID identification protocol, there exist other concerns surrounding the RFID technology. Some of them arise from the technology itself, such as distance checking, but others are related to the potential of RFID systems to gather huge amount of tracking data. Publishing and mining such moving objects data is essential to improve efficiency of supervisory control, assets management and localisation, transportation, etc. However, obvious privacy threats arise if an individual can be linked with some of those published trajectories. The present dissertation contributes to the design of algorithms and protocols aimed at dealing with the issues explained above. First, we propose a set of protocols and heuristics based on a distributed architecture that improve the efficiency of the identification process without compromising privacy or security. Moreover, we present a novel distance-bounding protocol based on graphs that is extremely low-resource consuming. Finally, we present two trajectory anonymisation methods aimed at preserving the individuals' privacy when their trajectories are released.